From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 May 2005 16:33:25 +0000 (+0000)
Subject: XML schema changes
X-Git-Tag: Release_2_0~197
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5a35786bf1c4219bfa00603036497a18486c6801;p=jalview.git

XML schema changes
---

diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
new file mode 100755
index 0000000..a51102b
--- /dev/null
+++ b/src/jalview/binding/Colour.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+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 Colour.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Colour implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _RGB
+     */
+    private java.lang.String _RGB;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Colour() {
+        super();
+    } //-- jalview.binding.Colour()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'RGB'.
+     * 
+     * @return String
+     * @return the value of field 'RGB'.
+     */
+    public java.lang.String getRGB()
+    {
+        return this._RGB;
+    } //-- java.lang.String getRGB() 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'RGB'.
+     * 
+     * @param RGB the value of field 'RGB'.
+     */
+    public void setRGB(java.lang.String RGB)
+    {
+        this._RGB = RGB;
+    } //-- void setRGB(java.lang.String) 
+
+    /**
+     * 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.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.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() 
+
+}
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 7f17893..61c80aa 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -50,6 +50,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _viewportList;
 
+    /**
+     * Field _userColoursList
+     */
+    private java.util.Vector _userColoursList;
+
 
       //----------------/
      //- Constructors -/
@@ -60,6 +65,7 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JSeqList = new Vector();
         _JGroupList = new Vector();
         _viewportList = new Vector();
+        _userColoursList = new Vector();
     } //-- jalview.binding.JalviewModelSequence()
 
 
@@ -122,6 +128,33 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void addJSeq(int, jalview.binding.JSeq) 
 
     /**
+     * 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
      * 
      * 
@@ -173,6 +206,18 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateJSeq() 
 
     /**
+     * Method enumerateUserColours
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateUserColours()
+    {
+        return _userColoursList.elements();
+    } //-- java.util.Enumeration enumerateUserColours() 
+
+    /**
      * Method enumerateViewport
      * 
      * 
@@ -281,6 +326,54 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- int getJSeqCount() 
 
     /**
+     * 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
      * 
      * 
@@ -393,6 +486,15 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() 
 
     /**
+     * Method removeAllUserColours
+     * 
+     */
+    public void removeAllUserColours()
+    {
+        _userColoursList.removeAllElements();
+    } //-- void removeAllUserColours() 
+
+    /**
      * Method removeAllViewport
      * 
      */
@@ -432,6 +534,21 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.JSeq removeJSeq(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
      * 
      * 
@@ -515,6 +632,40 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void setJSeq(jalview.binding.JSeq) 
 
     /**
+     * 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
      * 
      * 
diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java
new file mode 100755
index 0000000..36e5579
--- /dev/null
+++ b/src/jalview/binding/JalviewModelSequence2.java
@@ -0,0 +1,274 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- 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 JalviewModelSequence2.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence2 implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _items
+     */
+    private java.util.Vector _items;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelSequence2() {
+        super();
+        _items = new Vector();
+    } //-- jalview.binding.JalviewModelSequence2()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param vJalviewModelSequence2Item
+     */
+    public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _items.addElement(vJalviewModelSequence2Item);
+    } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
+
+    /**
+     * Method addJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJalviewModelSequence2Item
+     */
+    public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _items.insertElementAt(vJalviewModelSequence2Item, index);
+    } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
+
+    /**
+     * Method enumerateJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateJalviewModelSequence2Item()
+    {
+        return _items.elements();
+    } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() 
+
+    /**
+     * Method getJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param index
+     * @return JalviewModelSequence2Item
+     */
+    public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _items.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
+    } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) 
+
+    /**
+     * Method getJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @return JalviewModelSequence2Item
+     */
+    public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()
+    {
+        int size = _items.size();
+        jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() 
+
+    /**
+     * Method getJalviewModelSequence2ItemCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getJalviewModelSequence2ItemCount()
+    {
+        return _items.size();
+    } //-- int getJalviewModelSequence2ItemCount() 
+
+    /**
+     * 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 removeAllJalviewModelSequence2Item
+     * 
+     */
+    public void removeAllJalviewModelSequence2Item()
+    {
+        _items.removeAllElements();
+    } //-- void removeAllJalviewModelSequence2Item() 
+
+    /**
+     * Method removeJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param index
+     * @return JalviewModelSequence2Item
+     */
+    public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index)
+    {
+        java.lang.Object obj = _items.elementAt(index);
+        _items.removeElementAt(index);
+        return (jalview.binding.JalviewModelSequence2Item) obj;
+    } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) 
+
+    /**
+     * Method setJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJalviewModelSequence2Item
+     */
+    public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _items.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _items.setElementAt(vJalviewModelSequence2Item, index);
+    } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) 
+
+    /**
+     * Method setJalviewModelSequence2Item
+     * 
+     * 
+     * 
+     * @param jalviewModelSequence2ItemArray
+     */
+    public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)
+    {
+        //-- copy array
+        _items.removeAllElements();
+        for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {
+            _items.addElement(jalviewModelSequence2ItemArray[i]);
+        }
+    } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) 
+
+    /**
+     * 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.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.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() 
+
+}
diff --git a/src/jalview/binding/JalviewModelSequence2Item.java b/src/jalview/binding/JalviewModelSequence2Item.java
new file mode 100755
index 0000000..8678b09
--- /dev/null
+++ b/src/jalview/binding/JalviewModelSequence2Item.java
@@ -0,0 +1,197 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.Serializable;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModelSequence2Item.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence2Item implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _userColourSchemeList
+     */
+    private java.util.Vector _userColourSchemeList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelSequence2Item() {
+        super();
+        _userColourSchemeList = new Vector();
+    } //-- jalview.binding.JalviewModelSequence2Item()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addUserColourScheme
+     * 
+     * 
+     * 
+     * @param vUserColourScheme
+     */
+    public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColourSchemeList.addElement(vUserColourScheme);
+    } //-- void addUserColourScheme(jalview.binding.UserColourScheme) 
+
+    /**
+     * Method addUserColourScheme
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColourScheme
+     */
+    public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColourSchemeList.insertElementAt(vUserColourScheme, index);
+    } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) 
+
+    /**
+     * Method enumerateUserColourScheme
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateUserColourScheme()
+    {
+        return _userColourSchemeList.elements();
+    } //-- java.util.Enumeration enumerateUserColourScheme() 
+
+    /**
+     * Method getUserColourScheme
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColourScheme
+     */
+    public jalview.binding.UserColourScheme getUserColourScheme(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _userColourSchemeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);
+    } //-- jalview.binding.UserColourScheme getUserColourScheme(int) 
+
+    /**
+     * Method getUserColourScheme
+     * 
+     * 
+     * 
+     * @return UserColourScheme
+     */
+    public jalview.binding.UserColourScheme[] getUserColourScheme()
+    {
+        int size = _userColourSchemeList.size();
+        jalview.binding.UserColourScheme[] mArray = new jalview.binding.UserColourScheme[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.UserColourScheme[] getUserColourScheme() 
+
+    /**
+     * Method getUserColourSchemeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getUserColourSchemeCount()
+    {
+        return _userColourSchemeList.size();
+    } //-- int getUserColourSchemeCount() 
+
+    /**
+     * Method removeAllUserColourScheme
+     * 
+     */
+    public void removeAllUserColourScheme()
+    {
+        _userColourSchemeList.removeAllElements();
+    } //-- void removeAllUserColourScheme() 
+
+    /**
+     * Method removeUserColourScheme
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColourScheme
+     */
+    public jalview.binding.UserColourScheme removeUserColourScheme(int index)
+    {
+        java.lang.Object obj = _userColourSchemeList.elementAt(index);
+        _userColourSchemeList.removeElementAt(index);
+        return (jalview.binding.UserColourScheme) obj;
+    } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) 
+
+    /**
+     * Method setUserColourScheme
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColourScheme
+     */
+    public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _userColourSchemeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _userColourSchemeList.setElementAt(vUserColourScheme, index);
+    } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) 
+
+    /**
+     * Method setUserColourScheme
+     * 
+     * 
+     * 
+     * @param userColourSchemeArray
+     */
+    public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)
+    {
+        //-- copy array
+        _userColourSchemeList.removeAllElements();
+        for (int i = 0; i < userColourSchemeArray.length; i++) {
+            _userColourSchemeList.addElement(userColourSchemeArray[i]);
+        }
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
+
+}
diff --git a/src/jalview/binding/JalviewState.java b/src/jalview/binding/JalviewUserColours.java
similarity index 51%
rename from src/jalview/binding/JalviewState.java
rename to src/jalview/binding/JalviewUserColours.java
index ad9d1b3..676a623 100755
--- a/src/jalview/binding/JalviewState.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -15,7 +15,6 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
-import java.util.Date;
 import java.util.Enumeration;
 import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
@@ -25,11 +24,11 @@ import org.exolab.castor.xml.ValidationException;
 import org.xml.sax.ContentHandler;
 
 /**
- * Class JalviewState.
+ * Class JalviewUserColours.
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewState implements java.io.Serializable {
+public class JalviewUserColours implements java.io.Serializable {
 
 
       //--------------------------/
@@ -37,24 +36,19 @@ public class JalviewState implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _creationDate
+     * Field _colourList
      */
-    private java.util.Date _creationDate;
-
-    /**
-     * Field _fileList
-     */
-    private java.util.Vector _fileList;
+    private java.util.Vector _colourList;
 
 
       //----------------/
      //- Constructors -/
     //----------------/
 
-    public JalviewState() {
+    public JalviewUserColours() {
         super();
-        _fileList = new Vector();
-    } //-- jalview.binding.JalviewState()
+        _colourList = new Vector();
+    } //-- jalview.binding.JalviewUserColours()
 
 
       //-----------/
@@ -62,102 +56,91 @@ public class JalviewState implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addFile
+     * Method addColour
      * 
      * 
      * 
-     * @param vFile
+     * @param vColour
      */
-    public void addFile(java.lang.String vFile)
+    public void addColour(jalview.binding.Colour vColour)
         throws java.lang.IndexOutOfBoundsException
     {
-        _fileList.addElement(vFile);
-    } //-- void addFile(java.lang.String) 
+        _colourList.addElement(vColour);
+    } //-- void addColour(jalview.binding.Colour) 
 
     /**
-     * Method addFile
+     * Method addColour
      * 
      * 
      * 
      * @param index
-     * @param vFile
+     * @param vColour
      */
-    public void addFile(int index, java.lang.String vFile)
+    public void addColour(int index, jalview.binding.Colour vColour)
         throws java.lang.IndexOutOfBoundsException
     {
-        _fileList.insertElementAt(vFile, index);
-    } //-- void addFile(int, java.lang.String) 
+        _colourList.insertElementAt(vColour, index);
+    } //-- void addColour(int, jalview.binding.Colour) 
 
     /**
-     * Method enumerateFile
+     * Method enumerateColour
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateFile()
+    public java.util.Enumeration enumerateColour()
     {
-        return _fileList.elements();
-    } //-- java.util.Enumeration enumerateFile() 
+        return _colourList.elements();
+    } //-- java.util.Enumeration enumerateColour() 
 
     /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return Date
-     * @return the value of field 'creationDate'.
-     */
-    public java.util.Date getCreationDate()
-    {
-        return this._creationDate;
-    } //-- java.util.Date getCreationDate() 
-
-    /**
-     * Method getFile
+     * Method getColour
      * 
      * 
      * 
      * @param index
-     * @return String
+     * @return Colour
      */
-    public java.lang.String getFile(int index)
+    public jalview.binding.Colour getColour(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _fileList.size())) {
+        if ((index < 0) || (index > _colourList.size())) {
             throw new IndexOutOfBoundsException();
         }
         
-        return (String)_fileList.elementAt(index);
-    } //-- java.lang.String getFile(int) 
+        return (jalview.binding.Colour) _colourList.elementAt(index);
+    } //-- jalview.binding.Colour getColour(int) 
 
     /**
-     * Method getFile
+     * Method getColour
      * 
      * 
      * 
-     * @return String
+     * @return Colour
      */
-    public java.lang.String[] getFile()
+    public jalview.binding.Colour[] getColour()
     {
-        int size = _fileList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
+        int size = _colourList.size();
+        jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_fileList.elementAt(index);
+            mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);
         }
         return mArray;
-    } //-- java.lang.String[] getFile() 
+    } //-- jalview.binding.Colour[] getColour() 
 
     /**
-     * Method getFileCount
+     * Method getColourCount
      * 
      * 
      * 
      * @return int
      */
-    public int getFileCount()
+    public int getColourCount()
     {
-        return _fileList.size();
-    } //-- int getFileCount() 
+        return _colourList.size();
+    } //-- int getColourCount() 
 
     /**
      * Method isValid
@@ -206,72 +189,62 @@ public class JalviewState implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllFile
+     * Method removeAllColour
      * 
      */
-    public void removeAllFile()
+    public void removeAllColour()
     {
-        _fileList.removeAllElements();
-    } //-- void removeAllFile() 
+        _colourList.removeAllElements();
+    } //-- void removeAllColour() 
 
     /**
-     * Method removeFile
+     * Method removeColour
      * 
      * 
      * 
      * @param index
-     * @return String
-     */
-    public java.lang.String removeFile(int index)
-    {
-        java.lang.Object obj = _fileList.elementAt(index);
-        _fileList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeFile(int) 
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
+     * @return Colour
      */
-    public void setCreationDate(java.util.Date creationDate)
+    public jalview.binding.Colour removeColour(int index)
     {
-        this._creationDate = creationDate;
-    } //-- void setCreationDate(java.util.Date) 
+        java.lang.Object obj = _colourList.elementAt(index);
+        _colourList.removeElementAt(index);
+        return (jalview.binding.Colour) obj;
+    } //-- jalview.binding.Colour removeColour(int) 
 
     /**
-     * Method setFile
+     * Method setColour
      * 
      * 
      * 
      * @param index
-     * @param vFile
+     * @param vColour
      */
-    public void setFile(int index, java.lang.String vFile)
+    public void setColour(int index, jalview.binding.Colour vColour)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _fileList.size())) {
+        if ((index < 0) || (index > _colourList.size())) {
             throw new IndexOutOfBoundsException();
         }
-        _fileList.setElementAt(vFile, index);
-    } //-- void setFile(int, java.lang.String) 
+        _colourList.setElementAt(vColour, index);
+    } //-- void setColour(int, jalview.binding.Colour) 
 
     /**
-     * Method setFile
+     * Method setColour
      * 
      * 
      * 
-     * @param fileArray
+     * @param colourArray
      */
-    public void setFile(java.lang.String[] fileArray)
+    public void setColour(jalview.binding.Colour[] colourArray)
     {
         //-- copy array
-        _fileList.removeAllElements();
-        for (int i = 0; i < fileArray.length; i++) {
-            _fileList.addElement(fileArray[i]);
+        _colourList.removeAllElements();
+        for (int i = 0; i < colourArray.length; i++) {
+            _colourList.addElement(colourArray[i]);
         }
-    } //-- void setFile(java.lang.String) 
+    } //-- void setColour(jalview.binding.Colour) 
 
     /**
      * Method unmarshal
@@ -284,7 +257,7 @@ public class JalviewState implements java.io.Serializable {
     public static java.lang.Object unmarshal(java.io.Reader reader)
         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
     {
-        return (jalview.binding.JalviewState) Unmarshaller.unmarshal(jalview.binding.JalviewState.class, reader);
+        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
     } //-- java.lang.Object unmarshal(java.io.Reader) 
 
     /**
diff --git a/src/jalview/binding/JalviewUserColoursItem.java b/src/jalview/binding/JalviewUserColoursItem.java
new file mode 100755
index 0000000..ce6919c
--- /dev/null
+++ b/src/jalview/binding/JalviewUserColoursItem.java
@@ -0,0 +1,70 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.Serializable;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewUserColoursItem.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewUserColoursItem implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _colour
+     */
+    private jalview.binding.Colour _colour;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewUserColoursItem() {
+        super();
+    } //-- jalview.binding.JalviewUserColoursItem()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return Colour
+     * @return the value of field 'colour'.
+     */
+    public jalview.binding.Colour getColour()
+    {
+        return this._colour;
+    } //-- jalview.binding.Colour getColour() 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(jalview.binding.Colour colour)
+    {
+        this._colour = colour;
+    } //-- void setColour(jalview.binding.Colour) 
+
+}
diff --git a/src/jalview/binding/Residue.java b/src/jalview/binding/Residue.java
new file mode 100755
index 0000000..69e4312
--- /dev/null
+++ b/src/jalview/binding/Residue.java
@@ -0,0 +1,200 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+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 Residue.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Residue implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _RGB
+     */
+    private int _RGB;
+
+    /**
+     * keeps track of state for field: _RGB
+     */
+    private boolean _has_RGB;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Residue() {
+        super();
+    } //-- jalview.binding.Residue()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteRGB
+     * 
+     */
+    public void deleteRGB()
+    {
+        this._has_RGB= false;
+    } //-- void deleteRGB() 
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'RGB'.
+     * 
+     * @return int
+     * @return the value of field 'RGB'.
+     */
+    public int getRGB()
+    {
+        return this._RGB;
+    } //-- int getRGB() 
+
+    /**
+     * Method hasRGB
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasRGB()
+    {
+        return this._has_RGB;
+    } //-- boolean hasRGB() 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'RGB'.
+     * 
+     * @param RGB the value of field 'RGB'.
+     */
+    public void setRGB(int RGB)
+    {
+        this._RGB = RGB;
+        this._has_RGB = true;
+    } //-- void setRGB(int) 
+
+    /**
+     * 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.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.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() 
+
+}
diff --git a/src/jalview/binding/UserColour.java b/src/jalview/binding/UserColour.java
new file mode 100755
index 0000000..837d9af
--- /dev/null
+++ b/src/jalview/binding/UserColour.java
@@ -0,0 +1,200 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+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 UserColour.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColour implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private int _id;
+
+    /**
+     * keeps track of state for field: _id
+     */
+    private boolean _has_id;
+
+    /**
+     * Field _userColourScheme
+     */
+    private jalview.binding.UserColourScheme _userColourScheme;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColour() {
+        super();
+    } //-- jalview.binding.UserColour()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteId
+     * 
+     */
+    public void deleteId()
+    {
+        this._has_id= false;
+    } //-- void deleteId() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return int
+     * @return the value of field 'id'.
+     */
+    public int getId()
+    {
+        return this._id;
+    } //-- int getId() 
+
+    /**
+     * Returns the value of field 'userColourScheme'.
+     * 
+     * @return UserColourScheme
+     * @return the value of field 'userColourScheme'.
+     */
+    public jalview.binding.UserColourScheme getUserColourScheme()
+    {
+        return this._userColourScheme;
+    } //-- jalview.binding.UserColourScheme getUserColourScheme() 
+
+    /**
+     * Method hasId
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasId()
+    {
+        return this._has_id;
+    } //-- boolean hasId() 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(int id)
+    {
+        this._id = id;
+        this._has_id = true;
+    } //-- void setId(int) 
+
+    /**
+     * Sets the value of field 'userColourScheme'.
+     * 
+     * @param userColourScheme the value of field 'userColourScheme'
+     */
+    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)
+    {
+        this._userColourScheme = userColourScheme;
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
+
+    /**
+     * 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.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.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() 
+
+}
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
new file mode 100755
index 0000000..79ea637
--- /dev/null
+++ b/src/jalview/binding/UserColourScheme.java
@@ -0,0 +1,118 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+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 UserColourScheme.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColourScheme extends JalviewUserColours 
+implements java.io.Serializable
+{
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColourScheme() {
+        super();
+    } //-- jalview.binding.UserColourScheme()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 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 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.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.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() 
+
+}
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
new file mode 100755
index 0000000..241aaab
--- /dev/null
+++ b/src/jalview/binding/UserColours.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+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 UserColours.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColours implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _userColourScheme
+     */
+    private jalview.binding.UserColourScheme _userColourScheme;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColours() {
+        super();
+    } //-- jalview.binding.UserColours()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Returns the value of field 'userColourScheme'.
+     * 
+     * @return UserColourScheme
+     * @return the value of field 'userColourScheme'.
+     */
+    public jalview.binding.UserColourScheme getUserColourScheme()
+    {
+        return this._userColourScheme;
+    } //-- jalview.binding.UserColourScheme getUserColourScheme() 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Sets the value of field 'userColourScheme'.
+     * 
+     * @param userColourScheme the value of field 'userColourScheme'
+     */
+    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)
+    {
+        this._userColourScheme = userColourScheme;
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) 
+
+    /**
+     * 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.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.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() 
+
+}