X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewModelSequence.java;h=927f447bd4c8e13fab0fd279172a8f15bb52bdc9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=ba0c4c8adbc2e0d93c28e0d19db1c30b11acad3e;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
old mode 100755
new mode 100644
index ba0c4c8..927f447
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,948 +1,942 @@
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
-
-import org.exolab.castor.xml.*;
-
-/**
- * Class JalviewModelSequence.
- *
- * @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.schemabinding.version2.FeatureSettings _featureSettings;
-
-  //----------------/
-  //- 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
-   *
-   *
-   *
-   * @param vJGroup
-   */
-  public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JGroupList.addElement(vJGroup);
-  } //-- void addJGroup(jalview.schemabinding.version2.JGroup)
-
-  /**
-   * Method addJGroup
-   *
-   *
-   *
-   * @param index
-   * @param vJGroup
-   */
-  public void addJGroup(int index,
-                        jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JGroupList.insertElementAt(vJGroup, index);
-  } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup)
-
-  /**
-   * Method addJSeq
-   *
-   *
-   *
-   * @param vJSeq
-   */
-  public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JSeqList.addElement(vJSeq);
-  } //-- void addJSeq(jalview.schemabinding.version2.JSeq)
-
-  /**
-   * Method addJSeq
-   *
-   *
-   *
-   * @param index
-   * @param vJSeq
-   */
-  public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JSeqList.insertElementAt(vJSeq, index);
-  } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param vTree
-   */
-  public void addTree(jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.addElement(vTree);
-  } //-- void addTree(jalview.schemabinding.version2.Tree)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, jalview.schemabinding.version2.Tree)
-
-  /**
-   * Method addUserColours
-   *
-   *
-   *
-   * @param vUserColours
-   */
-  public void addUserColours(jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _userColoursList.addElement(vUserColours);
-  } //-- void addUserColours(jalview.schemabinding.version2.UserColours)
-
-  /**
-   * Method addUserColours
-   *
-   *
-   *
-   * @param index
-   * @param vUserColours
-   */
-  public void addUserColours(int index,
-                             jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _userColoursList.insertElementAt(vUserColours, index);
-  } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours)
-
-  /**
-   * Method addViewport
-   *
-   *
-   *
-   * @param vViewport
-   */
-  public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _viewportList.addElement(vViewport);
-  } //-- void addViewport(jalview.schemabinding.version2.Viewport)
-
-  /**
-   * Method addViewport
-   *
-   *
-   *
-   * @param index
-   * @param vViewport
-   */
-  public void addViewport(int index,
-                          jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _viewportList.insertElementAt(vViewport, index);
-  } //-- void addViewport(int, jalview.schemabinding.version2.Viewport)
-
-  /**
-   * Method enumerateJGroup
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateJGroup()
-  {
-    return _JGroupList.elements();
-  } //-- java.util.Enumeration enumerateJGroup()
-
-  /**
-   * Method enumerateJSeq
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateJSeq()
-  {
-    return _JSeqList.elements();
-  } //-- java.util.Enumeration enumerateJSeq()
-
-  /**
-   * Method enumerateTree
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateTree()
-  {
-    return _treeList.elements();
-  } //-- java.util.Enumeration enumerateTree()
-
-  /**
-   * Method enumerateUserColours
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateUserColours()
-  {
-    return _userColoursList.elements();
-  } //-- java.util.Enumeration enumerateUserColours()
-
-  /**
-   * Method enumerateViewport
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateViewport()
-  {
-    return _viewportList.elements();
-  } //-- java.util.Enumeration enumerateViewport()
-
-  /**
-   * Returns the value of field 'featureSettings'.
-   *
-   * @return FeatureSettings
-   * @return the value of field 'featureSettings'.
-   */
-  public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
-  {
-    return this._featureSettings;
-  } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
-
-  /**
-   * Method getJGroup
-   *
-   *
-   *
-   * @param index
-   * @return JGroup
-   */
-  public jalview.schemabinding.version2.JGroup getJGroup(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JGroupList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-  } //-- jalview.schemabinding.version2.JGroup getJGroup(int)
-
-  /**
-   * Method getJGroup
-   *
-   *
-   *
-   * @return JGroup
-   */
-  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()
-
-  /**
-   * Method getJGroupCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getJGroupCount()
-  {
-    return _JGroupList.size();
-  } //-- int getJGroupCount()
-
-  /**
-   * Method getJSeq
-   *
-   *
-   *
-   * @param index
-   * @return JSeq
-   */
-  public jalview.schemabinding.version2.JSeq getJSeq(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JSeqList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-  } //-- jalview.schemabinding.version2.JSeq getJSeq(int)
-
-  /**
-   * Method getJSeq
-   *
-   *
-   *
-   * @return JSeq
-   */
-  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()
-
-  /**
-   * Method getJSeqCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getJSeqCount()
-  {
-    return _JSeqList.size();
-  } //-- int getJSeqCount()
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @param index
-   * @return Tree
-   */
-  public jalview.schemabinding.version2.Tree getTree(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-  } //-- jalview.schemabinding.version2.Tree getTree(int)
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @return Tree
-   */
-  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()
-
-  /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getTreeCount()
-  {
-    return _treeList.size();
-  } //-- int getTreeCount()
-
-  /**
-   * Method getUserColours
-   *
-   *
-   *
-   * @param index
-   * @return UserColours
-   */
-  public jalview.schemabinding.version2.UserColours getUserColours(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _userColoursList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.schemabinding.version2.UserColours) _userColoursList.
-        elementAt(index);
-  } //-- jalview.schemabinding.version2.UserColours getUserColours(int)
-
-  /**
-   * Method getUserColours
-   *
-   *
-   *
-   * @return UserColours
-   */
-  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()
-
-  /**
-   * Method getUserColoursCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getUserColoursCount()
-  {
-    return _userColoursList.size();
-  } //-- int getUserColoursCount()
-
-  /**
-   * Method getViewport
-   *
-   *
-   *
-   * @param index
-   * @return Viewport
-   */
-  public jalview.schemabinding.version2.Viewport getViewport(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _viewportList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(
-        index);
-  } //-- jalview.schemabinding.version2.Viewport getViewport(int)
-
-  /**
-   * Method getViewport
-   *
-   *
-   *
-   * @return Viewport
-   */
-  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()
-
-  /**
-   * Method getViewportCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getViewportCount()
-  {
-    return _viewportList.size();
-  } //-- int getViewportCount()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    }
-    catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  } //-- boolean isValid()
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param out
-   */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param handler
-   */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, handler);
-  } //-- void marshal(org.xml.sax.ContentHandler)
-
-  /**
-   * Method removeAllJGroup
-   *
-   */
-  public void removeAllJGroup()
-  {
-    _JGroupList.removeAllElements();
-  } //-- void removeAllJGroup()
-
-  /**
-   * Method removeAllJSeq
-   *
-   */
-  public void removeAllJSeq()
-  {
-    _JSeqList.removeAllElements();
-  } //-- void removeAllJSeq()
-
-  /**
-   * Method removeAllTree
-   *
-   */
-  public void removeAllTree()
-  {
-    _treeList.removeAllElements();
-  } //-- void removeAllTree()
-
-  /**
-   * Method removeAllUserColours
-   *
-   */
-  public void removeAllUserColours()
-  {
-    _userColoursList.removeAllElements();
-  } //-- void removeAllUserColours()
-
-  /**
-   * Method removeAllViewport
-   *
-   */
-  public void removeAllViewport()
-  {
-    _viewportList.removeAllElements();
-  } //-- void removeAllViewport()
-
-  /**
-   * Method removeJGroup
-   *
-   *
-   *
-   * @param index
-   * @return JGroup
-   */
-  public jalview.schemabinding.version2.JGroup removeJGroup(int index)
-  {
-    java.lang.Object obj = _JGroupList.elementAt(index);
-    _JGroupList.removeElementAt(index);
-    return (jalview.schemabinding.version2.JGroup) obj;
-  } //-- jalview.schemabinding.version2.JGroup removeJGroup(int)
-
-  /**
-   * Method removeJSeq
-   *
-   *
-   *
-   * @param index
-   * @return JSeq
-   */
-  public jalview.schemabinding.version2.JSeq removeJSeq(int index)
-  {
-    java.lang.Object obj = _JSeqList.elementAt(index);
-    _JSeqList.removeElementAt(index);
-    return (jalview.schemabinding.version2.JSeq) obj;
-  } //-- jalview.schemabinding.version2.JSeq removeJSeq(int)
-
-  /**
-   * Method removeTree
-   *
-   *
-   *
-   * @param index
-   * @return Tree
-   */
-  public jalview.schemabinding.version2.Tree removeTree(int index)
-  {
-    java.lang.Object obj = _treeList.elementAt(index);
-    _treeList.removeElementAt(index);
-    return (jalview.schemabinding.version2.Tree) obj;
-  } //-- jalview.schemabinding.version2.Tree removeTree(int)
-
-  /**
-   * Method removeUserColours
-   *
-   *
-   *
-   * @param index
-   * @return UserColours
-   */
-  public jalview.schemabinding.version2.UserColours removeUserColours(int index)
-  {
-    java.lang.Object obj = _userColoursList.elementAt(index);
-    _userColoursList.removeElementAt(index);
-    return (jalview.schemabinding.version2.UserColours) obj;
-  } //-- jalview.schemabinding.version2.UserColours removeUserColours(int)
-
-  /**
-   * Method removeViewport
-   *
-   *
-   *
-   * @param index
-   * @return Viewport
-   */
-  public jalview.schemabinding.version2.Viewport removeViewport(int index)
-  {
-    java.lang.Object obj = _viewportList.elementAt(index);
-    _viewportList.removeElementAt(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'.
-   */
-  public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings
-                                 featureSettings)
-  {
-    this._featureSettings = featureSettings;
-  } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings)
-
-  /**
-   * Method setJGroup
-   *
-   *
-   *
-   * @param index
-   * @param vJGroup
-   */
-  public void setJGroup(int index,
-                        jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JGroupList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _JGroupList.setElementAt(vJGroup, index);
-  } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup)
-
-  /**
-   * Method setJGroup
-   *
-   *
-   *
-   * @param JGroupArray
-   */
-  public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
-  {
-    //-- copy array
-    _JGroupList.removeAllElements();
-    for (int i = 0; i < JGroupArray.length; i++)
-    {
-      _JGroupList.addElement(JGroupArray[i]);
-    }
-  } //-- void setJGroup(jalview.schemabinding.version2.JGroup)
-
-  /**
-   * Method setJSeq
-   *
-   *
-   *
-   * @param index
-   * @param vJSeq
-   */
-  public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JSeqList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _JSeqList.setElementAt(vJSeq, index);
-  } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq)
-
-  /**
-   * Method setJSeq
-   *
-   *
-   *
-   * @param JSeqArray
-   */
-  public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
-  {
-    //-- copy array
-    _JSeqList.removeAllElements();
-    for (int i = 0; i < JSeqArray.length; i++)
-    {
-      _JSeqList.addElement(JSeqArray[i]);
-    }
-  } //-- void setJSeq(jalview.schemabinding.version2.JSeq)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _treeList.setElementAt(vTree, index);
-  } //-- void setTree(int, jalview.schemabinding.version2.Tree)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param treeArray
-   */
-  public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
-  {
-    //-- copy array
-    _treeList.removeAllElements();
-    for (int i = 0; i < treeArray.length; i++)
-    {
-      _treeList.addElement(treeArray[i]);
-    }
-  } //-- void setTree(jalview.schemabinding.version2.Tree)
-
-  /**
-   * Method setUserColours
-   *
-   *
-   *
-   * @param index
-   * @param vUserColours
-   */
-  public void setUserColours(int index,
-                             jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _userColoursList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _userColoursList.setElementAt(vUserColours, index);
-  } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours)
-
-  /**
-   * Method setUserColours
-   *
-   *
-   *
-   * @param userColoursArray
-   */
-  public void setUserColours(jalview.schemabinding.version2.UserColours[]
-                             userColoursArray)
-  {
-    //-- copy array
-    _userColoursList.removeAllElements();
-    for (int i = 0; i < userColoursArray.length; i++)
-    {
-      _userColoursList.addElement(userColoursArray[i]);
-    }
-  } //-- void setUserColours(jalview.schemabinding.version2.UserColours)
-
-  /**
-   * Method setViewport
-   *
-   *
-   *
-   * @param index
-   * @param vViewport
-   */
-  public void setViewport(int index,
-                          jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _viewportList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _viewportList.setElementAt(vViewport, index);
-  } //-- void setViewport(int, jalview.schemabinding.version2.Viewport)
-
-  /**
-   * Method setViewport
-   *
-   *
-   *
-   * @param viewportArray
-   */
-  public void setViewport(jalview.schemabinding.version2.Viewport[]
-                          viewportArray)
-  {
-    //-- copy array
-    _viewportList.removeAllElements();
-    for (int i = 0; i < viewportArray.length; i++)
-    {
-      _viewportList.addElement(viewportArray[i]);
-    }
-  } //-- void setViewport(jalview.schemabinding.version2.Viewport)
-
-  /**
-   * 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();
-    validator.validate(this);
-  } //-- void validate()
-
-}
+/*******************************************************************************
+ * 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.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModelSequence.
+ * 
+ * @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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Viewport vViewport)
+    throws java.lang.IndexOutOfBoundsException {
+        this._viewportList.add(index, vViewport);
+    }
+
+    /**
+     * Method enumerateJGroup.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.JGroup elements
+     */
+    public java.util.Enumeration enumerateJGroup(
+    ) {
+        return this._JGroupList.elements();
+    }
+
+    /**
+     * Method enumerateJSeq.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.JSeq elements
+     */
+    public java.util.Enumeration enumerateJSeq(
+    ) {
+        return this._JSeqList.elements();
+    }
+
+    /**
+     * Method enumerateTree.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Tree elements
+     */
+    public java.util.Enumeration enumerateTree(
+    ) {
+        return this._treeList.elements();
+    }
+
+    /**
+     * Method enumerateUserColours.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.UserColours elements
+     */
+    public java.util.Enumeration enumerateUserColours(
+    ) {
+        return this._userColoursList.elements();
+    }
+
+    /**
+     * Method enumerateViewport.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JGroup at the given index
+     */
+    public jalview.schemabinding.version2.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.schemabinding.version2.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.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 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.schemabinding.version2.JSeq
+     * at the given index
+     */
+    public jalview.schemabinding.version2.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.schemabinding.version2.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.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 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.schemabinding.version2.Tree
+     * at the given index
+     */
+    public jalview.schemabinding.version2.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.schemabinding.version2.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.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 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.schemabinding.version2.UserColours at the given index
+     */
+    public jalview.schemabinding.version2.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.schemabinding.version2.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.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 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.schemabinding.version2.Viewport at the given index
+     */
+    public jalview.schemabinding.version2.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.schemabinding.version2.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.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 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.schemabinding.version2.JGroup vJGroup) {
+        boolean removed = _JGroupList.remove(vJGroup);
+        return removed;
+    }
+
+    /**
+     * Method removeJGroupAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.JGroup removeJGroupAt(
+            final int index) {
+        java.lang.Object obj = this._JGroupList.remove(index);
+        return (jalview.schemabinding.version2.JGroup) obj;
+    }
+
+    /**
+     * 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 the element removed from the collection
+     */
+    public jalview.schemabinding.version2.JSeq removeJSeqAt(
+            final int index) {
+        java.lang.Object obj = this._JSeqList.remove(index);
+        return (jalview.schemabinding.version2.JSeq) obj;
+    }
+
+    /**
+     * 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 removeTreeAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.Tree removeTreeAt(
+            final int index) {
+        java.lang.Object obj = this._treeList.remove(index);
+        return (jalview.schemabinding.version2.Tree) obj;
+    }
+
+    /**
+     * 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 the element removed from the collection
+     */
+    public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+            final int index) {
+        java.lang.Object obj = this._userColoursList.remove(index);
+        return (jalview.schemabinding.version2.UserColours) obj;
+    }
+
+    /**
+     * 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 the element removed from the collection
+     */
+    public jalview.schemabinding.version2.Viewport removeViewportAt(
+            final int index) {
+        java.lang.Object obj = this._viewportList.remove(index);
+        return (jalview.schemabinding.version2.Viewport) obj;
+    }
+
+    /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(
+            final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.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);
+    }
+
+}