X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=e4f6c5aa988a21545ce4e8cf38c394fe3f2234a8;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=f8207ebfaf1b13b1cbe982721dadf512024d23c6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
old mode 100755
new mode 100644
index f8207eb..e4f6c5a
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,24 +1,31 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview 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 3 of the License, or (at your option) any later version.
- * 
+ *
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.binding;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -29,937 +36,904 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _JSeqList.
-   */
-  private java.util.Vector _JSeqList;
-
-  /**
-   * Field _JGroupList.
-   */
-  private java.util.Vector _JGroupList;
-
-  /**
-   * Field _viewportList.
-   */
-  private java.util.Vector _viewportList;
-
-  /**
-   * Field _userColoursList.
-   */
-  private java.util.Vector _userColoursList;
-
-  /**
-   * Field _treeList.
-   */
-  private java.util.Vector _treeList;
-
-  /**
-   * Field _featureSettings.
-   */
-  private jalview.binding.FeatureSettings _featureSettings;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public JalviewModelSequence()
-  {
-    super();
-    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(final jalview.binding.JGroup vJGroup)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._JGroupList.addElement(vJGroup);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vJGroup
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addJGroup(final int index,
-          final jalview.binding.JGroup vJGroup)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._JGroupList.add(index, vJGroup);
-  }
-
-  /**
-   * 
-   * 
-   * @param vJSeq
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addJSeq(final jalview.binding.JSeq vJSeq)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._JSeqList.addElement(vJSeq);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vJSeq
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._JSeqList.add(index, vJSeq);
-  }
-
-  /**
-   * 
-   * 
-   * @param vTree
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addTree(final jalview.binding.Tree vTree)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._treeList.addElement(vTree);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vTree
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addTree(final int index, final jalview.binding.Tree vTree)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._treeList.add(index, vTree);
-  }
-
-  /**
-   * 
-   * 
-   * @param vUserColours
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addUserColours(final jalview.binding.UserColours vUserColours)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._userColoursList.addElement(vUserColours);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vUserColours
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addUserColours(final int index,
-          final jalview.binding.UserColours vUserColours)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._userColoursList.add(index, vUserColours);
-  }
-
-  /**
-   * 
-   * 
-   * @param vViewport
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addViewport(final jalview.binding.Viewport vViewport)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._viewportList.addElement(vViewport);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vViewport
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addViewport(final int index,
-          final jalview.binding.Viewport vViewport)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._viewportList.add(index, vViewport);
-  }
-
-  /**
-   * Method enumerateJGroup.
-   * 
-   * @return an Enumeration over all jalview.binding.JGroup elements
-   */
-  public java.util.Enumeration enumerateJGroup()
-  {
-    return this._JGroupList.elements();
-  }
-
-  /**
-   * Method enumerateJSeq.
-   * 
-   * @return an Enumeration over all jalview.binding.JSeq elements
-   */
-  public java.util.Enumeration enumerateJSeq()
-  {
-    return this._JSeqList.elements();
-  }
-
-  /**
-   * Method enumerateTree.
-   * 
-   * @return an Enumeration over all jalview.binding.Tree elements
-   */
-  public java.util.Enumeration enumerateTree()
-  {
-    return this._treeList.elements();
-  }
-
-  /**
-   * Method enumerateUserColours.
-   * 
-   * @return an Enumeration over all jalview.binding.UserColours elements
-   */
-  public java.util.Enumeration enumerateUserColours()
-  {
-    return this._userColoursList.elements();
-  }
-
-  /**
-   * Method enumerateViewport.
-   * 
-   * @return an Enumeration over all jalview.binding.Viewport elements
-   */
-  public java.util.Enumeration enumerateViewport()
-  {
-    return this._viewportList.elements();
-  }
-
-  /**
-   * Returns the value of field 'featureSettings'.
-   * 
-   * @return the value of field 'FeatureSettings'.
-   */
-  public jalview.binding.FeatureSettings getFeatureSettings()
-  {
-    return this._featureSettings;
-  }
-
-  /**
-   * Method getJGroup.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.binding.JGroup at the given index
-   */
-  public jalview.binding.JGroup getJGroup(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._JGroupList.size())
-    {
-      throw new IndexOutOfBoundsException("getJGroup: Index value '"
-              + index + "' not in range [0.."
-              + (this._JGroupList.size() - 1) + "]");
-    }
-
-    return (jalview.binding.JGroup) _JGroupList.get(index);
-  }
-
-  /**
-   * 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.binding.JGroup[] getJGroup()
-  {
-    jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
-    return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
-  }
-
-  /**
-   * Method getJGroupCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getJGroupCount()
-  {
-    return this._JGroupList.size();
-  }
-
-  /**
-   * Method getJSeq.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.binding.JSeq at the given index
-   */
-  public jalview.binding.JSeq getJSeq(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._JSeqList.size())
-    {
-      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
-              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-    }
-
-    return (jalview.binding.JSeq) _JSeqList.get(index);
-  }
-
-  /**
-   * 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.binding.JSeq[] getJSeq()
-  {
-    jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
-    return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
-  }
-
-  /**
-   * Method getJSeqCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getJSeqCount()
-  {
-    return this._JSeqList.size();
-  }
-
-  /**
-   * Method getTree.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.binding.Tree at the given index
-   */
-  public jalview.binding.Tree getTree(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._treeList.size())
-    {
-      throw new IndexOutOfBoundsException("getTree: Index value '" + index
-              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-    }
-
-    return (jalview.binding.Tree) _treeList.get(index);
-  }
-
-  /**
-   * 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.binding.Tree[] getTree()
-  {
-    jalview.binding.Tree[] array = new jalview.binding.Tree[0];
-    return (jalview.binding.Tree[]) this._treeList.toArray(array);
-  }
-
-  /**
-   * Method getTreeCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getTreeCount()
-  {
-    return this._treeList.size();
-  }
-
-  /**
-   * Method getUserColours.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.binding.UserColours at the given index
-   */
-  public jalview.binding.UserColours getUserColours(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._userColoursList.size())
-    {
-      throw new IndexOutOfBoundsException("getUserColours: Index value '"
-              + index + "' not in range [0.."
-              + (this._userColoursList.size() - 1) + "]");
-    }
-
-    return (jalview.binding.UserColours) _userColoursList.get(index);
-  }
-
-  /**
-   * 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.binding.UserColours[] getUserColours()
-  {
-    jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
-    return (jalview.binding.UserColours[]) this._userColoursList
-            .toArray(array);
-  }
-
-  /**
-   * Method getUserColoursCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getUserColoursCount()
-  {
-    return this._userColoursList.size();
-  }
-
-  /**
-   * Method getViewport.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.binding.Viewport at the given index
-   */
-  public jalview.binding.Viewport getViewport(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._viewportList.size())
-    {
-      throw new IndexOutOfBoundsException("getViewport: Index value '"
-              + index + "' not in range [0.."
-              + (this._viewportList.size() - 1) + "]");
-    }
-
-    return (jalview.binding.Viewport) _viewportList.get(index);
-  }
-
-  /**
-   * 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.binding.Viewport[] getViewport()
-  {
-    jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
-    return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
-  }
-
-  /**
-   * Method getViewportCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getViewportCount()
-  {
-    return this._viewportList.size();
-  }
-
-  /**
-   * 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 removeAllJGroup()
-  {
-    this._JGroupList.clear();
-  }
-
-  /**
-     */
-  public void removeAllJSeq()
-  {
-    this._JSeqList.clear();
-  }
-
-  /**
-     */
-  public void removeAllTree()
-  {
-    this._treeList.clear();
-  }
-
-  /**
-     */
-  public void removeAllUserColours()
-  {
-    this._userColoursList.clear();
-  }
-
-  /**
-     */
-  public void removeAllViewport()
-  {
-    this._viewportList.clear();
-  }
-
-  /**
-   * Method removeJGroup.
-   * 
-   * @param vJGroup
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
-  {
-    boolean removed = _JGroupList.remove(vJGroup);
-    return removed;
-  }
-
-  /**
-   * Method removeJGroupAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.binding.JGroup removeJGroupAt(final int index)
-  {
-    java.lang.Object obj = this._JGroupList.remove(index);
-    return (jalview.binding.JGroup) obj;
-  }
-
-  /**
-   * Method removeJSeq.
-   * 
-   * @param vJSeq
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
-  {
-    boolean removed = _JSeqList.remove(vJSeq);
-    return removed;
-  }
-
-  /**
-   * Method removeJSeqAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.binding.JSeq removeJSeqAt(final int index)
-  {
-    java.lang.Object obj = this._JSeqList.remove(index);
-    return (jalview.binding.JSeq) obj;
-  }
-
-  /**
-   * Method removeTree.
-   * 
-   * @param vTree
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeTree(final jalview.binding.Tree vTree)
-  {
-    boolean removed = _treeList.remove(vTree);
-    return removed;
-  }
-
-  /**
-   * Method removeTreeAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.binding.Tree removeTreeAt(final int index)
-  {
-    java.lang.Object obj = this._treeList.remove(index);
-    return (jalview.binding.Tree) obj;
-  }
-
-  /**
-   * Method removeUserColours.
-   * 
-   * @param vUserColours
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeUserColours(
-          final jalview.binding.UserColours vUserColours)
-  {
-    boolean removed = _userColoursList.remove(vUserColours);
-    return removed;
-  }
-
-  /**
-   * Method removeUserColoursAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.binding.UserColours removeUserColoursAt(final int index)
-  {
-    java.lang.Object obj = this._userColoursList.remove(index);
-    return (jalview.binding.UserColours) obj;
-  }
-
-  /**
-   * Method removeViewport.
-   * 
-   * @param vViewport
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeViewport(final jalview.binding.Viewport vViewport)
-  {
-    boolean removed = _viewportList.remove(vViewport);
-    return removed;
-  }
-
-  /**
-   * Method removeViewportAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.binding.Viewport removeViewportAt(final int index)
-  {
-    java.lang.Object obj = this._viewportList.remove(index);
-    return (jalview.binding.Viewport) obj;
-  }
-
-  /**
-   * Sets the value of field 'featureSettings'.
-   * 
-   * @param featureSettings
-   *          the value of field 'featureSettings'.
-   */
-  public void setFeatureSettings(
-          final jalview.binding.FeatureSettings featureSettings)
-  {
-    this._featureSettings = featureSettings;
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vJGroup
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setJGroup(final int index,
-          final jalview.binding.JGroup vJGroup)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._JGroupList.size())
-    {
-      throw new IndexOutOfBoundsException("setJGroup: Index value '"
-              + index + "' not in range [0.."
-              + (this._JGroupList.size() - 1) + "]");
-    }
-
-    this._JGroupList.set(index, vJGroup);
-  }
-
-  /**
-   * 
-   * 
-   * @param vJGroupArray
-   */
-  public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
-  {
-    // -- copy array
-    _JGroupList.clear();
-
-    for (int i = 0; i < vJGroupArray.length; i++)
-    {
-      this._JGroupList.add(vJGroupArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vJSeq
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._JSeqList.size())
-    {
-      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
-              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-    }
-
-    this._JSeqList.set(index, vJSeq);
-  }
-
-  /**
-   * 
-   * 
-   * @param vJSeqArray
-   */
-  public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
-  {
-    // -- copy array
-    _JSeqList.clear();
-
-    for (int i = 0; i < vJSeqArray.length; i++)
-    {
-      this._JSeqList.add(vJSeqArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vTree
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setTree(final int index, final jalview.binding.Tree vTree)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._treeList.size())
-    {
-      throw new IndexOutOfBoundsException("setTree: Index value '" + index
-              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-    }
-
-    this._treeList.set(index, vTree);
-  }
-
-  /**
-   * 
-   * 
-   * @param vTreeArray
-   */
-  public void setTree(final jalview.binding.Tree[] vTreeArray)
-  {
-    // -- copy array
-    _treeList.clear();
-
-    for (int i = 0; i < vTreeArray.length; i++)
-    {
-      this._treeList.add(vTreeArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vUserColours
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setUserColours(final int index,
-          final jalview.binding.UserColours vUserColours)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._userColoursList.size())
-    {
-      throw new IndexOutOfBoundsException("setUserColours: Index value '"
-              + index + "' not in range [0.."
-              + (this._userColoursList.size() - 1) + "]");
-    }
-
-    this._userColoursList.set(index, vUserColours);
-  }
-
-  /**
-   * 
-   * 
-   * @param vUserColoursArray
-   */
-  public void setUserColours(
-          final jalview.binding.UserColours[] vUserColoursArray)
-  {
-    // -- copy array
-    _userColoursList.clear();
-
-    for (int i = 0; i < vUserColoursArray.length; i++)
-    {
-      this._userColoursList.add(vUserColoursArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vViewport
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setViewport(final int index,
-          final jalview.binding.Viewport vViewport)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._viewportList.size())
-    {
-      throw new IndexOutOfBoundsException("setViewport: Index value '"
-              + index + "' not in range [0.."
-              + (this._viewportList.size() - 1) + "]");
-    }
-
-    this._viewportList.set(index, vViewport);
-  }
-
-  /**
-   * 
-   * 
-   * @param vViewportArray
-   */
-  public void setViewport(final jalview.binding.Viewport[] vViewportArray)
-  {
-    // -- copy array
-    _viewportList.clear();
-
-    for (int i = 0; i < vViewportArray.length; i++)
-    {
-      this._viewportList.add(vViewportArray[i]);
-    }
-  }
-
-  /**
-   * 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 jalview.binding.JalviewModelSequence
-   */
-  public static jalview.binding.JalviewModelSequence unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
-            jalview.binding.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);
-  }
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _JSeqList.
+     */
+    private java.util.Vector _JSeqList;
+
+    /**
+     * Field _JGroupList.
+     */
+    private java.util.Vector _JGroupList;
+
+    /**
+     * Field _viewportList.
+     */
+    private java.util.Vector _viewportList;
+
+    /**
+     * Field _userColoursList.
+     */
+    private java.util.Vector _userColoursList;
+
+    /**
+     * Field _treeList.
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _featureSettings.
+     */
+    private jalview.binding.FeatureSettings _featureSettings;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelSequence() {
+        super();
+        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(
+            final jalview.binding.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JGroupList.addElement(vJGroup);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addJGroup(
+            final int index,
+            final jalview.binding.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JGroupList.add(index, vJGroup);
+    }
+
+    /**
+     * 
+     * 
+     * @param vJSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addJSeq(
+            final jalview.binding.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JSeqList.addElement(vJSeq);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addJSeq(
+            final int index,
+            final jalview.binding.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._JSeqList.add(index, vJSeq);
+    }
+
+    /**
+     * 
+     * 
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTree(
+            final jalview.binding.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.addElement(vTree);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addTree(
+            final int index,
+            final jalview.binding.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        this._treeList.add(index, vTree);
+    }
+
+    /**
+     * 
+     * 
+     * @param vUserColours
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addUserColours(
+            final jalview.binding.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        this._userColoursList.addElement(vUserColours);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addUserColours(
+            final int index,
+            final jalview.binding.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        this._userColoursList.add(index, vUserColours);
+    }
+
+    /**
+     * 
+     * 
+     * @param vViewport
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addViewport(
+            final jalview.binding.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        this._viewportList.addElement(vViewport);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addViewport(
+            final int index,
+            final jalview.binding.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        this._viewportList.add(index, vViewport);
+    }
+
+    /**
+     * Method enumerateJGroup.
+     * 
+     * @return an Enumeration over all jalview.binding.JGroup
+     * elements
+     */
+    public java.util.Enumeration enumerateJGroup(
+    ) {
+        return this._JGroupList.elements();
+    }
+
+    /**
+     * Method enumerateJSeq.
+     * 
+     * @return an Enumeration over all jalview.binding.JSeq elements
+     */
+    public java.util.Enumeration enumerateJSeq(
+    ) {
+        return this._JSeqList.elements();
+    }
+
+    /**
+     * Method enumerateTree.
+     * 
+     * @return an Enumeration over all jalview.binding.Tree elements
+     */
+    public java.util.Enumeration enumerateTree(
+    ) {
+        return this._treeList.elements();
+    }
+
+    /**
+     * Method enumerateUserColours.
+     * 
+     * @return an Enumeration over all jalview.binding.UserColours
+     * elements
+     */
+    public java.util.Enumeration enumerateUserColours(
+    ) {
+        return this._userColoursList.elements();
+    }
+
+    /**
+     * Method enumerateViewport.
+     * 
+     * @return an Enumeration over all jalview.binding.Viewport
+     * elements
+     */
+    public java.util.Enumeration enumerateViewport(
+    ) {
+        return this._viewportList.elements();
+    }
+
+    /**
+     * Returns the value of field 'featureSettings'.
+     * 
+     * @return the value of field 'FeatureSettings'.
+     */
+    public jalview.binding.FeatureSettings getFeatureSettings(
+    ) {
+        return this._featureSettings;
+    }
+
+    /**
+     * Method getJGroup.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.JGroup at the given
+     * index
+     */
+    public jalview.binding.JGroup getJGroup(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JGroupList.size()) {
+            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.JGroup) _JGroupList.get(index);
+    }
+
+    /**
+     * 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.binding.JGroup[] getJGroup(
+    ) {
+        jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+        return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+    }
+
+    /**
+     * Method getJGroupCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getJGroupCount(
+    ) {
+        return this._JGroupList.size();
+    }
+
+    /**
+     * Method getJSeq.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.JSeq at the given
+     * index
+     */
+    public jalview.binding.JSeq getJSeq(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JSeqList.size()) {
+            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.JSeq) _JSeqList.get(index);
+    }
+
+    /**
+     * 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.binding.JSeq[] getJSeq(
+    ) {
+        jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+        return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+    }
+
+    /**
+     * Method getJSeqCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getJSeqCount(
+    ) {
+        return this._JSeqList.size();
+    }
+
+    /**
+     * Method getTree.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.Tree at the given
+     * index
+     */
+    public jalview.binding.Tree getTree(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treeList.size()) {
+            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.Tree) _treeList.get(index);
+    }
+
+    /**
+     * 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.binding.Tree[] getTree(
+    ) {
+        jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+        return (jalview.binding.Tree[]) this._treeList.toArray(array);
+    }
+
+    /**
+     * Method getTreeCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getTreeCount(
+    ) {
+        return this._treeList.size();
+    }
+
+    /**
+     * Method getUserColours.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.UserColours at the
+     * given index
+     */
+    public jalview.binding.UserColours getUserColours(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._userColoursList.size()) {
+            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.UserColours) _userColoursList.get(index);
+    }
+
+    /**
+     * 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.binding.UserColours[] getUserColours(
+    ) {
+        jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+        return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
+    }
+
+    /**
+     * Method getUserColoursCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getUserColoursCount(
+    ) {
+        return this._userColoursList.size();
+    }
+
+    /**
+     * Method getViewport.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.Viewport at the
+     * given index
+     */
+    public jalview.binding.Viewport getViewport(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._viewportList.size()) {
+            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.Viewport) _viewportList.get(index);
+    }
+
+    /**
+     * 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.binding.Viewport[] getViewport(
+    ) {
+        jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+        return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+    }
+
+    /**
+     * Method getViewportCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getViewportCount(
+    ) {
+        return this._viewportList.size();
+    }
+
+    /**
+     * 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 removeAllJGroup(
+    ) {
+        this._JGroupList.clear();
+    }
+
+    /**
+     */
+    public void removeAllJSeq(
+    ) {
+        this._JSeqList.clear();
+    }
+
+    /**
+     */
+    public void removeAllTree(
+    ) {
+        this._treeList.clear();
+    }
+
+    /**
+     */
+    public void removeAllUserColours(
+    ) {
+        this._userColoursList.clear();
+    }
+
+    /**
+     */
+    public void removeAllViewport(
+    ) {
+        this._viewportList.clear();
+    }
+
+    /**
+     * Method removeJGroup.
+     * 
+     * @param vJGroup
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeJGroup(
+            final jalview.binding.JGroup vJGroup) {
+        boolean removed = _JGroupList.remove(vJGroup);
+        return removed;
+    }
+
+    /**
+     * Method removeJGroupAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.JGroup removeJGroupAt(
+            final int index) {
+        java.lang.Object obj = this._JGroupList.remove(index);
+        return (jalview.binding.JGroup) obj;
+    }
+
+    /**
+     * Method removeJSeq.
+     * 
+     * @param vJSeq
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeJSeq(
+            final jalview.binding.JSeq vJSeq) {
+        boolean removed = _JSeqList.remove(vJSeq);
+        return removed;
+    }
+
+    /**
+     * Method removeJSeqAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.JSeq removeJSeqAt(
+            final int index) {
+        java.lang.Object obj = this._JSeqList.remove(index);
+        return (jalview.binding.JSeq) obj;
+    }
+
+    /**
+     * Method removeTree.
+     * 
+     * @param vTree
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeTree(
+            final jalview.binding.Tree vTree) {
+        boolean removed = _treeList.remove(vTree);
+        return removed;
+    }
+
+    /**
+     * Method removeTreeAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.Tree removeTreeAt(
+            final int index) {
+        java.lang.Object obj = this._treeList.remove(index);
+        return (jalview.binding.Tree) obj;
+    }
+
+    /**
+     * Method removeUserColours.
+     * 
+     * @param vUserColours
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeUserColours(
+            final jalview.binding.UserColours vUserColours) {
+        boolean removed = _userColoursList.remove(vUserColours);
+        return removed;
+    }
+
+    /**
+     * Method removeUserColoursAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.UserColours removeUserColoursAt(
+            final int index) {
+        java.lang.Object obj = this._userColoursList.remove(index);
+        return (jalview.binding.UserColours) obj;
+    }
+
+    /**
+     * Method removeViewport.
+     * 
+     * @param vViewport
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeViewport(
+            final jalview.binding.Viewport vViewport) {
+        boolean removed = _viewportList.remove(vViewport);
+        return removed;
+    }
+
+    /**
+     * Method removeViewportAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.Viewport removeViewportAt(
+            final int index) {
+        java.lang.Object obj = this._viewportList.remove(index);
+        return (jalview.binding.Viewport) obj;
+    }
+
+    /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(
+            final jalview.binding.FeatureSettings featureSettings) {
+        this._featureSettings = featureSettings;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setJGroup(
+            final int index,
+            final jalview.binding.JGroup vJGroup)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JGroupList.size()) {
+            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+        }
+        
+        this._JGroupList.set(index, vJGroup);
+    }
+
+    /**
+     * 
+     * 
+     * @param vJGroupArray
+     */
+    public void setJGroup(
+            final jalview.binding.JGroup[] vJGroupArray) {
+        //-- copy array
+        _JGroupList.clear();
+        
+        for (int i = 0; i < vJGroupArray.length; i++) {
+                this._JGroupList.add(vJGroupArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setJSeq(
+            final int index,
+            final jalview.binding.JSeq vJSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._JSeqList.size()) {
+            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+        }
+        
+        this._JSeqList.set(index, vJSeq);
+    }
+
+    /**
+     * 
+     * 
+     * @param vJSeqArray
+     */
+    public void setJSeq(
+            final jalview.binding.JSeq[] vJSeqArray) {
+        //-- copy array
+        _JSeqList.clear();
+        
+        for (int i = 0; i < vJSeqArray.length; i++) {
+                this._JSeqList.add(vJSeqArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vTree
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setTree(
+            final int index,
+            final jalview.binding.Tree vTree)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._treeList.size()) {
+            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+        }
+        
+        this._treeList.set(index, vTree);
+    }
+
+    /**
+     * 
+     * 
+     * @param vTreeArray
+     */
+    public void setTree(
+            final jalview.binding.Tree[] vTreeArray) {
+        //-- copy array
+        _treeList.clear();
+        
+        for (int i = 0; i < vTreeArray.length; i++) {
+                this._treeList.add(vTreeArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setUserColours(
+            final int index,
+            final jalview.binding.UserColours vUserColours)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._userColoursList.size()) {
+            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+        }
+        
+        this._userColoursList.set(index, vUserColours);
+    }
+
+    /**
+     * 
+     * 
+     * @param vUserColoursArray
+     */
+    public void setUserColours(
+            final jalview.binding.UserColours[] vUserColoursArray) {
+        //-- copy array
+        _userColoursList.clear();
+        
+        for (int i = 0; i < vUserColoursArray.length; i++) {
+                this._userColoursList.add(vUserColoursArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setViewport(
+            final int index,
+            final jalview.binding.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._viewportList.size()) {
+            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+        }
+        
+        this._viewportList.set(index, vViewport);
+    }
+
+    /**
+     * 
+     * 
+     * @param vViewportArray
+     */
+    public void setViewport(
+            final jalview.binding.Viewport[] vViewportArray) {
+        //-- copy array
+        _viewportList.clear();
+        
+        for (int i = 0; i < vViewportArray.length; i++) {
+                this._viewportList.add(vViewportArray[i]);
+        }
+    }
+
+    /**
+     * 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 jalview.binding.JalviewModelSequence
+     */
+    public static jalview.binding.JalviewModelSequence unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.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);
+    }
 
 }