X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=cbb50d51d53666f8e3fc80a9c4672c4cf7c39ca4;hb=95ebd2cf76003f52476a7802c99831dfa98945f7;hp=2abee137b05dec5a1f34cd8a54e84cd63e3b87ef;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 2abee13..cbb50d5 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,56 +1,38 @@
 /*
- * 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.
  * $Id$
  */
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.binding;
-
-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;
+package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
+
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
-
 import java.util.Enumeration;
 import java.util.Vector;
-
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
 
 /**
  * Class JalviewModelSequence.
- *
+ * 
  * @version $Revision$ $Date$
  */
 public class JalviewModelSequence implements java.io.Serializable {
-    //--------------------------/
-    //- Class/Member Variables -/
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -73,683 +55,850 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _userColoursList;
 
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _featureSettings
+     */
+    private jalview.binding.FeatureSettings _featureSettings;
+
+
+      //----------------/
+     //- Constructors -/
     //----------------/
-    //- Constructors -/
-    //----------------/
+
     public JalviewModelSequence() {
         super();
         _JSeqList = new Vector();
         _JGroupList = new Vector();
         _viewportList = new Vector();
         _userColoursList = new Vector();
-    }
-     //-- jalview.binding.JalviewModelSequence()
- //-----------/
+        _treeList = new Vector();
+    } //-- jalview.binding.JalviewModelSequence()
+
 
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addJGroup
+     * 
+     * 
+     * 
+     * @param vJGroup
+     */
     public void addJGroup(jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _JGroupList.addElement(vJGroup);
-    }
-     //-- void addJGroup(jalview.binding.JGroup)
+    } //-- void addJGroup(jalview.binding.JGroup) 
 
     /**
      * Method addJGroup
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vJGroup
      */
     public void addJGroup(int index, jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _JGroupList.insertElementAt(vJGroup, index);
-    }
-     //-- void addJGroup(int, jalview.binding.JGroup)
+    } //-- void addJGroup(int, jalview.binding.JGroup) 
 
     /**
      * Method addJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param vJSeq
      */
     public void addJSeq(jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _JSeqList.addElement(vJSeq);
-    }
-     //-- void addJSeq(jalview.binding.JSeq)
+    } //-- void addJSeq(jalview.binding.JSeq) 
 
     /**
      * Method addJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vJSeq
      */
     public void addJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _JSeqList.insertElementAt(vJSeq, index);
-    }
-     //-- void addJSeq(int, jalview.binding.JSeq)
+    } //-- 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 {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _userColoursList.addElement(vUserColours);
-    }
-     //-- void addUserColours(jalview.binding.UserColours)
+    } //-- void addUserColours(jalview.binding.UserColours) 
 
     /**
      * Method addUserColours
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vUserColours
      */
-    public void addUserColours(int index,
-        jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException {
+    public void addUserColours(int index, jalview.binding.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
         _userColoursList.insertElementAt(vUserColours, index);
-    }
-     //-- void addUserColours(int, jalview.binding.UserColours)
+    } //-- void addUserColours(int, jalview.binding.UserColours) 
 
     /**
      * Method addViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param vViewport
      */
     public void addViewport(jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _viewportList.addElement(vViewport);
-    }
-     //-- void addViewport(jalview.binding.Viewport)
+    } //-- void addViewport(jalview.binding.Viewport) 
 
     /**
      * Method addViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vViewport
      */
     public void addViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException {
+        throws java.lang.IndexOutOfBoundsException
+    {
         _viewportList.insertElementAt(vViewport, index);
-    }
-     //-- void addViewport(int, jalview.binding.Viewport)
+    } //-- void addViewport(int, jalview.binding.Viewport) 
 
     /**
      * Method enumerateJGroup
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateJGroup() {
+    public java.util.Enumeration enumerateJGroup()
+    {
         return _JGroupList.elements();
-    }
-     //-- java.util.Enumeration enumerateJGroup()
+    } //-- java.util.Enumeration enumerateJGroup() 
 
     /**
      * Method enumerateJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateJSeq() {
+    public java.util.Enumeration enumerateJSeq()
+    {
         return _JSeqList.elements();
-    }
-     //-- java.util.Enumeration enumerateJSeq()
+    } //-- 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() {
+    public java.util.Enumeration enumerateUserColours()
+    {
         return _userColoursList.elements();
-    }
-     //-- java.util.Enumeration enumerateUserColours()
+    } //-- java.util.Enumeration enumerateUserColours() 
 
     /**
      * Method enumerateViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateViewport() {
+    public java.util.Enumeration enumerateViewport()
+    {
         return _viewportList.elements();
-    }
-     //-- java.util.Enumeration enumerateViewport()
+    } //-- 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 {
+        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)
+    } //-- jalview.binding.JGroup getJGroup(int) 
 
     /**
      * Method getJGroup
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return JGroup
      */
-    public jalview.binding.JGroup[] getJGroup() {
+    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()
+    } //-- jalview.binding.JGroup[] getJGroup() 
 
     /**
      * Method getJGroupCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getJGroupCount() {
+    public int getJGroupCount()
+    {
         return _JGroupList.size();
-    }
-     //-- int getJGroupCount()
+    } //-- int getJGroupCount() 
 
     /**
      * Method getJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return JSeq
      */
     public jalview.binding.JSeq getJSeq(int index)
-        throws java.lang.IndexOutOfBoundsException {
+        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)
+    } //-- jalview.binding.JSeq getJSeq(int) 
 
     /**
      * Method getJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return JSeq
      */
-    public jalview.binding.JSeq[] getJSeq() {
+    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()
+    } //-- jalview.binding.JSeq[] getJSeq() 
 
     /**
      * Method getJSeqCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getJSeqCount() {
+    public int getJSeqCount()
+    {
         return _JSeqList.size();
-    }
-     //-- int getJSeqCount()
+    } //-- 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 {
+        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)
+    } //-- jalview.binding.UserColours getUserColours(int) 
 
     /**
      * Method getUserColours
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return UserColours
      */
-    public jalview.binding.UserColours[] getUserColours() {
+    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()
+    } //-- jalview.binding.UserColours[] getUserColours() 
 
     /**
      * Method getUserColoursCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getUserColoursCount() {
+    public int getUserColoursCount()
+    {
         return _userColoursList.size();
-    }
-     //-- int getUserColoursCount()
+    } //-- int getUserColoursCount() 
 
     /**
      * Method getViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return Viewport
      */
     public jalview.binding.Viewport getViewport(int index)
-        throws java.lang.IndexOutOfBoundsException {
+        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)
+    } //-- jalview.binding.Viewport getViewport(int) 
 
     /**
      * Method getViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return Viewport
      */
-    public jalview.binding.Viewport[] getViewport() {
+    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()
+    } //-- jalview.binding.Viewport[] getViewport() 
 
     /**
      * Method getViewportCount
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getViewportCount() {
+    public int getViewportCount()
+    {
         return _viewportList.size();
-    }
-     //-- int getViewportCount()
+    } //-- int getViewportCount() 
 
     /**
      * Method isValid
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
-    public boolean isValid() {
+    public boolean isValid()
+    {
         try {
             validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
             return false;
         }
-
         return true;
-    }
-     //-- boolean isValid()
+    } //-- boolean isValid() 
 
     /**
      * Method marshal
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, 
-            org.exolab.castor.xml.ValidationException {
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
         Marshaller.marshal(this, out);
-    }
-     //-- void marshal(java.io.Writer)
+    } //-- void marshal(java.io.Writer) 
 
     /**
      * Method marshal
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
-            org.exolab.castor.xml.ValidationException {
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
         Marshaller.marshal(this, handler);
-    }
-     //-- void marshal(org.xml.sax.ContentHandler)
+    } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
      * Method removeAllJGroup
-     *
+     * 
      */
-    public void removeAllJGroup() {
+    public void removeAllJGroup()
+    {
         _JGroupList.removeAllElements();
-    }
-     //-- void removeAllJGroup()
+    } //-- void removeAllJGroup() 
 
     /**
      * Method removeAllJSeq
-     *
+     * 
      */
-    public void removeAllJSeq() {
+    public void removeAllJSeq()
+    {
         _JSeqList.removeAllElements();
-    }
-     //-- void removeAllJSeq()
+    } //-- void removeAllJSeq() 
+
+    /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
 
     /**
      * Method removeAllUserColours
-     *
+     * 
      */
-    public void removeAllUserColours() {
+    public void removeAllUserColours()
+    {
         _userColoursList.removeAllElements();
-    }
-     //-- void removeAllUserColours()
+    } //-- void removeAllUserColours() 
 
     /**
      * Method removeAllViewport
-     *
+     * 
      */
-    public void removeAllViewport() {
+    public void removeAllViewport()
+    {
         _viewportList.removeAllElements();
-    }
-     //-- void removeAllViewport()
+    } //-- void removeAllViewport() 
 
     /**
      * Method removeJGroup
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return JGroup
      */
-    public jalview.binding.JGroup removeJGroup(int index) {
+    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)
+    } //-- jalview.binding.JGroup removeJGroup(int) 
 
     /**
      * Method removeJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return JSeq
      */
-    public jalview.binding.JSeq removeJSeq(int index) {
+    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)
+    } //-- 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) {
+    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)
+    } //-- jalview.binding.UserColours removeUserColours(int) 
 
     /**
      * Method removeViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @return Viewport
      */
-    public jalview.binding.Viewport removeViewport(int index) {
+    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)
+    } //-- 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 {
+        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)
+    } //-- void setJGroup(int, jalview.binding.JGroup) 
 
     /**
      * Method setJGroup
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param JGroupArray
      */
-    public void setJGroup(jalview.binding.JGroup[] 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)
+    } //-- void setJGroup(jalview.binding.JGroup) 
 
     /**
      * Method setJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vJSeq
      */
     public void setJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException {
+        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)
+    } //-- void setJSeq(int, jalview.binding.JSeq) 
 
     /**
      * Method setJSeq
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param JSeqArray
      */
-    public void setJSeq(jalview.binding.JSeq[] 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)
+    } //-- 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 {
+    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)
+    } //-- void setUserColours(int, jalview.binding.UserColours) 
 
     /**
      * Method setUserColours
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param userColoursArray
      */
-    public void setUserColours(jalview.binding.UserColours[] 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)
+    } //-- void setUserColours(jalview.binding.UserColours) 
 
     /**
      * Method setViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @param vViewport
      */
     public void setViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException {
+        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)
+    } //-- void setViewport(int, jalview.binding.Viewport) 
 
     /**
      * Method setViewport
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param viewportArray
      */
-    public void setViewport(jalview.binding.Viewport[] 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)
+    } //-- 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)
+        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 {
+    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()
+    } //-- void validate() 
+
 }