X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=cbb50d51d53666f8e3fc80a9c4672c4cf7c39ca4;hb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;hp=2c2abff3ffcdd703e49ac569b643aafe6a80a735;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 2c2abff..cbb50d5 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with
+ * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,894 +7,898 @@
 
 package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
 
-import org.exolab.castor.xml.*;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
 
 /**
  * Class 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;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public JalviewModelSequence()
-  {
-    super();
-    _JSeqList = new Vector();
-    _JGroupList = new Vector();
-    _viewportList = new Vector();
-    _userColoursList = new Vector();
-    _treeList = new Vector();
-  } //-- jalview.binding.JalviewModelSequence()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addJGroup
-   *
-   *
-   *
-   * @param vJGroup
-   */
-  public void addJGroup(jalview.binding.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JGroupList.addElement(vJGroup);
-  } //-- void addJGroup(jalview.binding.JGroup)
-
-  /**
-   * Method addJGroup
-   *
-   *
-   *
-   * @param index
-   * @param vJGroup
-   */
-  public void addJGroup(int index, jalview.binding.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JGroupList.insertElementAt(vJGroup, index);
-  } //-- void addJGroup(int, jalview.binding.JGroup)
-
-  /**
-   * Method addJSeq
-   *
-   *
-   *
-   * @param vJSeq
-   */
-  public void addJSeq(jalview.binding.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JSeqList.addElement(vJSeq);
-  } //-- void addJSeq(jalview.binding.JSeq)
-
-  /**
-   * Method addJSeq
-   *
-   *
-   *
-   * @param index
-   * @param vJSeq
-   */
-  public void addJSeq(int index, jalview.binding.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _JSeqList.insertElementAt(vJSeq, index);
-  } //-- void addJSeq(int, jalview.binding.JSeq)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param vTree
-   */
-  public void addTree(jalview.binding.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.addElement(vTree);
-  } //-- void addTree(jalview.binding.Tree)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void addTree(int index, jalview.binding.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, jalview.binding.Tree)
-
-  /**
-   * Method addUserColours
-   *
-   *
-   *
-   * @param vUserColours
-   */
-  public void addUserColours(jalview.binding.UserColours vUserColours)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _userColoursList.addElement(vUserColours);
-  } //-- void addUserColours(jalview.binding.UserColours)
-
-  /**
-   * Method addUserColours
-   *
-   *
-   *
-   * @param index
-   * @param vUserColours
-   */
-  public void addUserColours(int index,
-                             jalview.binding.UserColours vUserColours)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _userColoursList.insertElementAt(vUserColours, index);
-  } //-- void addUserColours(int, jalview.binding.UserColours)
-
-  /**
-   * Method addViewport
-   *
-   *
-   *
-   * @param vViewport
-   */
-  public void addViewport(jalview.binding.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _viewportList.addElement(vViewport);
-  } //-- void addViewport(jalview.binding.Viewport)
-
-  /**
-   * Method addViewport
-   *
-   *
-   *
-   * @param index
-   * @param vViewport
-   */
-  public void addViewport(int index, jalview.binding.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _viewportList.insertElementAt(vViewport, index);
-  } //-- void addViewport(int, jalview.binding.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()
-
-  /**
-   * Method getJGroup
-   *
-   *
-   *
-   * @param index
-   * @return JGroup
-   */
-  public jalview.binding.JGroup getJGroup(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JGroupList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.JGroup) _JGroupList.elementAt(index);
-  } //-- jalview.binding.JGroup getJGroup(int)
-
-  /**
-   * Method getJGroup
-   *
-   *
-   *
-   * @return JGroup
-   */
-  public jalview.binding.JGroup[] getJGroup()
-  {
-    int size = _JGroupList.size();
-    jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.binding.JGroup[] getJGroup()
-
-  /**
-   * Method getJGroupCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getJGroupCount()
-  {
-    return _JGroupList.size();
-  } //-- int getJGroupCount()
-
-  /**
-   * Method getJSeq
-   *
-   *
-   *
-   * @param index
-   * @return JSeq
-   */
-  public jalview.binding.JSeq getJSeq(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JSeqList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.JSeq) _JSeqList.elementAt(index);
-  } //-- jalview.binding.JSeq getJSeq(int)
-
-  /**
-   * Method getJSeq
-   *
-   *
-   *
-   * @return JSeq
-   */
-  public jalview.binding.JSeq[] getJSeq()
-  {
-    int size = _JSeqList.size();
-    jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.binding.JSeq[] getJSeq()
-
-  /**
-   * Method getJSeqCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getJSeqCount()
-  {
-    return _JSeqList.size();
-  } //-- int getJSeqCount()
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @param index
-   * @return Tree
-   */
-  public jalview.binding.Tree getTree(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.Tree) _treeList.elementAt(index);
-  } //-- jalview.binding.Tree getTree(int)
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @return Tree
-   */
-  public jalview.binding.Tree[] getTree()
-  {
-    int size = _treeList.size();
-    jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.binding.Tree[] getTree()
-
-  /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getTreeCount()
-  {
-    return _treeList.size();
-  } //-- int getTreeCount()
-
-  /**
-   * Method getUserColours
-   *
-   *
-   *
-   * @param index
-   * @return UserColours
-   */
-  public jalview.binding.UserColours getUserColours(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _userColoursList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.UserColours) _userColoursList.elementAt(index);
-  } //-- jalview.binding.UserColours getUserColours(int)
-
-  /**
-   * Method getUserColours
-   *
-   *
-   *
-   * @return UserColours
-   */
-  public jalview.binding.UserColours[] getUserColours()
-  {
-    int size = _userColoursList.size();
-    jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(
-          index);
-    }
-    return mArray;
-  } //-- jalview.binding.UserColours[] getUserColours()
-
-  /**
-   * Method getUserColoursCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getUserColoursCount()
-  {
-    return _userColoursList.size();
-  } //-- int getUserColoursCount()
-
-  /**
-   * Method getViewport
-   *
-   *
-   *
-   * @param index
-   * @return Viewport
-   */
-  public jalview.binding.Viewport getViewport(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _viewportList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.Viewport) _viewportList.elementAt(index);
-  } //-- jalview.binding.Viewport getViewport(int)
-
-  /**
-   * Method getViewport
-   *
-   *
-   *
-   * @return Viewport
-   */
-  public jalview.binding.Viewport[] getViewport()
-  {
-    int size = _viewportList.size();
-    jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.binding.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.binding.JGroup removeJGroup(int index)
-  {
-    java.lang.Object obj = _JGroupList.elementAt(index);
-    _JGroupList.removeElementAt(index);
-    return (jalview.binding.JGroup) obj;
-  } //-- jalview.binding.JGroup removeJGroup(int)
-
-  /**
-   * Method removeJSeq
-   *
-   *
-   *
-   * @param index
-   * @return JSeq
-   */
-  public jalview.binding.JSeq removeJSeq(int index)
-  {
-    java.lang.Object obj = _JSeqList.elementAt(index);
-    _JSeqList.removeElementAt(index);
-    return (jalview.binding.JSeq) obj;
-  } //-- jalview.binding.JSeq removeJSeq(int)
-
-  /**
-   * Method removeTree
-   *
-   *
-   *
-   * @param index
-   * @return Tree
-   */
-  public jalview.binding.Tree removeTree(int index)
-  {
-    java.lang.Object obj = _treeList.elementAt(index);
-    _treeList.removeElementAt(index);
-    return (jalview.binding.Tree) obj;
-  } //-- jalview.binding.Tree removeTree(int)
-
-  /**
-   * Method removeUserColours
-   *
-   *
-   *
-   * @param index
-   * @return UserColours
-   */
-  public jalview.binding.UserColours removeUserColours(int index)
-  {
-    java.lang.Object obj = _userColoursList.elementAt(index);
-    _userColoursList.removeElementAt(index);
-    return (jalview.binding.UserColours) obj;
-  } //-- jalview.binding.UserColours removeUserColours(int)
-
-  /**
-   * Method removeViewport
-   *
-   *
-   *
-   * @param index
-   * @return Viewport
-   */
-  public jalview.binding.Viewport removeViewport(int index)
-  {
-    java.lang.Object obj = _viewportList.elementAt(index);
-    _viewportList.removeElementAt(index);
-    return (jalview.binding.Viewport) obj;
-  } //-- jalview.binding.Viewport removeViewport(int)
-
-  /**
-   * Method setJGroup
-   *
-   *
-   *
-   * @param index
-   * @param vJGroup
-   */
-  public void setJGroup(int index, jalview.binding.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.binding.JGroup)
-
-  /**
-   * Method setJGroup
-   *
-   *
-   *
-   * @param JGroupArray
-   */
-  public void setJGroup(jalview.binding.JGroup[] JGroupArray)
-  {
-    //-- copy array
-    _JGroupList.removeAllElements();
-    for (int i = 0; i < JGroupArray.length; i++)
-    {
-      _JGroupList.addElement(JGroupArray[i]);
-    }
-  } //-- void setJGroup(jalview.binding.JGroup)
-
-  /**
-   * Method setJSeq
-   *
-   *
-   *
-   * @param index
-   * @param vJSeq
-   */
-  public void setJSeq(int index, jalview.binding.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.binding.JSeq)
-
-  /**
-   * Method setJSeq
-   *
-   *
-   *
-   * @param JSeqArray
-   */
-  public void setJSeq(jalview.binding.JSeq[] JSeqArray)
-  {
-    //-- copy array
-    _JSeqList.removeAllElements();
-    for (int i = 0; i < JSeqArray.length; i++)
-    {
-      _JSeqList.addElement(JSeqArray[i]);
-    }
-  } //-- void setJSeq(jalview.binding.JSeq)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void setTree(int index, jalview.binding.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.binding.Tree)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param treeArray
-   */
-  public void setTree(jalview.binding.Tree[] treeArray)
-  {
-    //-- copy array
-    _treeList.removeAllElements();
-    for (int i = 0; i < treeArray.length; i++)
-    {
-      _treeList.addElement(treeArray[i]);
-    }
-  } //-- void setTree(jalview.binding.Tree)
-
-  /**
-   * Method setUserColours
-   *
-   *
-   *
-   * @param index
-   * @param vUserColours
-   */
-  public void setUserColours(int index,
-                             jalview.binding.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.binding.UserColours)
-
-  /**
-   * Method setUserColours
-   *
-   *
-   *
-   * @param userColoursArray
-   */
-  public void setUserColours(jalview.binding.UserColours[] userColoursArray)
-  {
-    //-- copy array
-    _userColoursList.removeAllElements();
-    for (int i = 0; i < userColoursArray.length; i++)
-    {
-      _userColoursList.addElement(userColoursArray[i]);
-    }
-  } //-- void setUserColours(jalview.binding.UserColours)
-
-  /**
-   * Method setViewport
-   *
-   *
-   *
-   * @param index
-   * @param vViewport
-   */
-  public void setViewport(int index, jalview.binding.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.binding.Viewport)
-
-  /**
-   * Method setViewport
-   *
-   *
-   *
-   * @param viewportArray
-   */
-  public void setViewport(jalview.binding.Viewport[] viewportArray)
-  {
-    //-- copy array
-    _viewportList.removeAllElements();
-    for (int i = 0; i < viewportArray.length; i++)
-    {
-      _viewportList.addElement(viewportArray[i]);
-    }
-  } //-- void setViewport(jalview.binding.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.binding.JalviewModelSequence) Unmarshaller.unmarshal(
-        jalview.binding.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()
+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();
+        _JSeqList = new Vector();
+        _JGroupList = new Vector();
+        _viewportList = new Vector();
+        _userColoursList = new Vector();
+        _treeList = new Vector();
+    } //-- jalview.binding.JalviewModelSequence()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addJGroup
+     * 
+     * 
+     * 
+     * @param vJGroup
+     */
+    public void addJGroup(jalview.binding.JGroup vJGroup)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JGroupList.addElement(vJGroup);
+    } //-- void addJGroup(jalview.binding.JGroup) 
+
+    /**
+     * Method addJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     */
+    public void addJGroup(int index, jalview.binding.JGroup vJGroup)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JGroupList.insertElementAt(vJGroup, index);
+    } //-- void addJGroup(int, jalview.binding.JGroup) 
+
+    /**
+     * Method addJSeq
+     * 
+     * 
+     * 
+     * @param vJSeq
+     */
+    public void addJSeq(jalview.binding.JSeq vJSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JSeqList.addElement(vJSeq);
+    } //-- void addJSeq(jalview.binding.JSeq) 
+
+    /**
+     * Method addJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     */
+    public void addJSeq(int index, jalview.binding.JSeq vJSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JSeqList.insertElementAt(vJSeq, index);
+    } //-- void addJSeq(int, jalview.binding.JSeq) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(jalview.binding.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(jalview.binding.Tree) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, jalview.binding.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, jalview.binding.Tree) 
+
+    /**
+     * Method addUserColours
+     * 
+     * 
+     * 
+     * @param vUserColours
+     */
+    public void addUserColours(jalview.binding.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColoursList.addElement(vUserColours);
+    } //-- void addUserColours(jalview.binding.UserColours) 
+
+    /**
+     * Method addUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     */
+    public void addUserColours(int index, jalview.binding.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColoursList.insertElementAt(vUserColours, index);
+    } //-- void addUserColours(int, jalview.binding.UserColours) 
+
+    /**
+     * Method addViewport
+     * 
+     * 
+     * 
+     * @param vViewport
+     */
+    public void addViewport(jalview.binding.Viewport vViewport)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _viewportList.addElement(vViewport);
+    } //-- void addViewport(jalview.binding.Viewport) 
+
+    /**
+     * Method addViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     */
+    public void addViewport(int index, jalview.binding.Viewport vViewport)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _viewportList.insertElementAt(vViewport, index);
+    } //-- void addViewport(int, jalview.binding.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.binding.FeatureSettings getFeatureSettings()
+    {
+        return this._featureSettings;
+    } //-- jalview.binding.FeatureSettings getFeatureSettings() 
+
+    /**
+     * Method getJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @return JGroup
+     */
+    public jalview.binding.JGroup getJGroup(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JGroupList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.JGroup) _JGroupList.elementAt(index);
+    } //-- jalview.binding.JGroup getJGroup(int) 
+
+    /**
+     * Method getJGroup
+     * 
+     * 
+     * 
+     * @return JGroup
+     */
+    public jalview.binding.JGroup[] getJGroup()
+    {
+        int size = _JGroupList.size();
+        jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.JGroup[] getJGroup() 
+
+    /**
+     * Method getJGroupCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getJGroupCount()
+    {
+        return _JGroupList.size();
+    } //-- int getJGroupCount() 
+
+    /**
+     * Method getJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return JSeq
+     */
+    public jalview.binding.JSeq getJSeq(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JSeqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.JSeq) _JSeqList.elementAt(index);
+    } //-- jalview.binding.JSeq getJSeq(int) 
+
+    /**
+     * Method getJSeq
+     * 
+     * 
+     * 
+     * @return JSeq
+     */
+    public jalview.binding.JSeq[] getJSeq()
+    {
+        int size = _JSeqList.size();
+        jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.JSeq[] getJSeq() 
+
+    /**
+     * Method getJSeqCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getJSeqCount()
+    {
+        return _JSeqList.size();
+    } //-- int getJSeqCount() 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.binding.Tree getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Tree) _treeList.elementAt(index);
+    } //-- jalview.binding.Tree getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @return Tree
+     */
+    public jalview.binding.Tree[] getTree()
+    {
+        int size = _treeList.size();
+        jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Tree[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
+
+    /**
+     * Method getUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColours
+     */
+    public jalview.binding.UserColours getUserColours(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _userColoursList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.UserColours) _userColoursList.elementAt(index);
+    } //-- jalview.binding.UserColours getUserColours(int) 
+
+    /**
+     * Method getUserColours
+     * 
+     * 
+     * 
+     * @return UserColours
+     */
+    public jalview.binding.UserColours[] getUserColours()
+    {
+        int size = _userColoursList.size();
+        jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.UserColours[] getUserColours() 
+
+    /**
+     * Method getUserColoursCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getUserColoursCount()
+    {
+        return _userColoursList.size();
+    } //-- int getUserColoursCount() 
+
+    /**
+     * Method getViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @return Viewport
+     */
+    public jalview.binding.Viewport getViewport(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _viewportList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Viewport) _viewportList.elementAt(index);
+    } //-- jalview.binding.Viewport getViewport(int) 
+
+    /**
+     * Method getViewport
+     * 
+     * 
+     * 
+     * @return Viewport
+     */
+    public jalview.binding.Viewport[] getViewport()
+    {
+        int size = _viewportList.size();
+        jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.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.binding.JGroup removeJGroup(int index)
+    {
+        java.lang.Object obj = _JGroupList.elementAt(index);
+        _JGroupList.removeElementAt(index);
+        return (jalview.binding.JGroup) obj;
+    } //-- jalview.binding.JGroup removeJGroup(int) 
+
+    /**
+     * Method removeJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return JSeq
+     */
+    public jalview.binding.JSeq removeJSeq(int index)
+    {
+        java.lang.Object obj = _JSeqList.elementAt(index);
+        _JSeqList.removeElementAt(index);
+        return (jalview.binding.JSeq) obj;
+    } //-- jalview.binding.JSeq removeJSeq(int) 
+
+    /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.binding.Tree removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (jalview.binding.Tree) obj;
+    } //-- jalview.binding.Tree removeTree(int) 
+
+    /**
+     * Method removeUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColours
+     */
+    public jalview.binding.UserColours removeUserColours(int index)
+    {
+        java.lang.Object obj = _userColoursList.elementAt(index);
+        _userColoursList.removeElementAt(index);
+        return (jalview.binding.UserColours) obj;
+    } //-- jalview.binding.UserColours removeUserColours(int) 
+
+    /**
+     * Method removeViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @return Viewport
+     */
+    public jalview.binding.Viewport removeViewport(int index)
+    {
+        java.lang.Object obj = _viewportList.elementAt(index);
+        _viewportList.removeElementAt(index);
+        return (jalview.binding.Viewport) obj;
+    } //-- jalview.binding.Viewport removeViewport(int) 
+
+    /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)
+    {
+        this._featureSettings = featureSettings;
+    } //-- void setFeatureSettings(jalview.binding.FeatureSettings) 
+
+    /**
+     * Method setJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     */
+    public void setJGroup(int index, jalview.binding.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.binding.JGroup) 
+
+    /**
+     * Method setJGroup
+     * 
+     * 
+     * 
+     * @param JGroupArray
+     */
+    public void setJGroup(jalview.binding.JGroup[] JGroupArray)
+    {
+        //-- copy array
+        _JGroupList.removeAllElements();
+        for (int i = 0; i < JGroupArray.length; i++) {
+            _JGroupList.addElement(JGroupArray[i]);
+        }
+    } //-- void setJGroup(jalview.binding.JGroup) 
+
+    /**
+     * Method setJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     */
+    public void setJSeq(int index, jalview.binding.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.binding.JSeq) 
+
+    /**
+     * Method setJSeq
+     * 
+     * 
+     * 
+     * @param JSeqArray
+     */
+    public void setJSeq(jalview.binding.JSeq[] JSeqArray)
+    {
+        //-- copy array
+        _JSeqList.removeAllElements();
+        for (int i = 0; i < JSeqArray.length; i++) {
+            _JSeqList.addElement(JSeqArray[i]);
+        }
+    } //-- void setJSeq(jalview.binding.JSeq) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, jalview.binding.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.binding.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(jalview.binding.Tree[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(jalview.binding.Tree) 
+
+    /**
+     * Method setUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     */
+    public void setUserColours(int index, jalview.binding.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.binding.UserColours) 
+
+    /**
+     * Method setUserColours
+     * 
+     * 
+     * 
+     * @param userColoursArray
+     */
+    public void setUserColours(jalview.binding.UserColours[] userColoursArray)
+    {
+        //-- copy array
+        _userColoursList.removeAllElements();
+        for (int i = 0; i < userColoursArray.length; i++) {
+            _userColoursList.addElement(userColoursArray[i]);
+        }
+    } //-- void setUserColours(jalview.binding.UserColours) 
+
+    /**
+     * Method setViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     */
+    public void setViewport(int index, jalview.binding.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.binding.Viewport) 
+
+    /**
+     * Method setViewport
+     * 
+     * 
+     * 
+     * @param viewportArray
+     */
+    public void setViewport(jalview.binding.Viewport[] viewportArray)
+    {
+        //-- copy array
+        _viewportList.removeAllElements();
+        for (int i = 0; i < viewportArray.length; i++) {
+            _viewportList.addElement(viewportArray[i]);
+        }
+    } //-- void setViewport(jalview.binding.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.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.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() 
 
 }