XML schema changes

diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
new file mode 100755 (executable)
index 0000000..a51102b
--- /dev/null
+++ b/src/jalview/binding/Colour.java
@@ -0,0 +1,173 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Colour.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Colour implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+    /**\r
+     * Field _RGB\r
+     */\r
+    private java.lang.String _RGB;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Colour() {\r
+        super();\r
+    } //-- jalview.binding.Colour()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'RGB'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'RGB'.\r
+     */\r
+    public java.lang.String getRGB()\r
+    {\r
+        return this._RGB;\r
+    } //-- java.lang.String getRGB() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'RGB'.\r
+     * \r
+     * @param RGB the value of field 'RGB'.\r
+     */\r
+    public void setRGB(java.lang.String RGB)\r
+    {\r
+        this._RGB = RGB;\r
+    } //-- void setRGB(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 7f17893..61c80aa 100755 (executable)
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -50,6 +50,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */\r
     private java.util.Vector _viewportList;\r
 \r
+    /**\r
+     * Field _userColoursList\r
+     */\r
+    private java.util.Vector _userColoursList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -60,6 +65,7 @@ public class JalviewModelSequence implements java.io.Serializable {
         _JSeqList = new Vector();\r
         _JGroupList = new Vector();\r
         _viewportList = new Vector();\r
+        _userColoursList = new Vector();\r
     } //-- jalview.binding.JalviewModelSequence()\r
 \r
 \r
@@ -122,6 +128,33 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void addJSeq(int, jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.addElement(vUserColours);\r
+    } //-- void addUserColours(jalview.binding.UserColours) \r
+\r
+    /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.insertElementAt(vUserColours, index);\r
+    } //-- void addUserColours(int, jalview.binding.UserColours) \r
+\r
+    /**\r
      * Method addViewport\r
      * \r
      * \r
@@ -173,6 +206,18 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateJSeq() \r
 \r
     /**\r
+     * Method enumerateUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateUserColours()\r
+    {\r
+        return _userColoursList.elements();\r
+    } //-- java.util.Enumeration enumerateUserColours() \r
+\r
+    /**\r
      * Method enumerateViewport\r
      * \r
      * \r
@@ -281,6 +326,54 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- int getJSeqCount() \r
 \r
     /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours getUserColours(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+    } //-- jalview.binding.UserColours getUserColours(int) \r
+\r
+    /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours[] getUserColours()\r
+    {\r
+        int size = _userColoursList.size();\r
+        jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.UserColours[] getUserColours() \r
+\r
+    /**\r
+     * Method getUserColoursCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getUserColoursCount()\r
+    {\r
+        return _userColoursList.size();\r
+    } //-- int getUserColoursCount() \r
+\r
+    /**\r
      * Method getViewport\r
      * \r
      * \r
@@ -393,6 +486,15 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void removeAllJSeq() \r
 \r
     /**\r
+     * Method removeAllUserColours\r
+     * \r
+     */\r
+    public void removeAllUserColours()\r
+    {\r
+        _userColoursList.removeAllElements();\r
+    } //-- void removeAllUserColours() \r
+\r
+    /**\r
      * Method removeAllViewport\r
      * \r
      */\r
@@ -432,6 +534,21 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.JSeq removeJSeq(int) \r
 \r
     /**\r
+     * Method removeUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.binding.UserColours removeUserColours(int index)\r
+    {\r
+        java.lang.Object obj = _userColoursList.elementAt(index);\r
+        _userColoursList.removeElementAt(index);\r
+        return (jalview.binding.UserColours) obj;\r
+    } //-- jalview.binding.UserColours removeUserColours(int) \r
+\r
+    /**\r
      * Method removeViewport\r
      * \r
      * \r
@@ -515,6 +632,40 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- void setJSeq(jalview.binding.JSeq) \r
 \r
     /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _userColoursList.setElementAt(vUserColours, index);\r
+    } //-- void setUserColours(int, jalview.binding.UserColours) \r
+\r
+    /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param userColoursArray\r
+     */\r
+    public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
+    {\r
+        //-- copy array\r
+        _userColoursList.removeAllElements();\r
+        for (int i = 0; i < userColoursArray.length; i++) {\r
+            _userColoursList.addElement(userColoursArray[i]);\r
+        }\r
+    } //-- void setUserColours(jalview.binding.UserColours) \r
+\r
+    /**\r
      * Method setViewport\r
      * \r
      * \r

diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java
new file mode 100755 (executable)
index 0000000..36e5579
--- /dev/null
+++ b/src/jalview/binding/JalviewModelSequence2.java
@@ -0,0 +1,274 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class JalviewModelSequence2.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewModelSequence2 implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _items\r
+     */\r
+    private java.util.Vector _items;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModelSequence2() {\r
+        super();\r
+        _items = new Vector();\r
+    } //-- jalview.binding.JalviewModelSequence2()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param vJalviewModelSequence2Item\r
+     */\r
+    public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _items.addElement(vJalviewModelSequence2Item);\r
+    } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
+\r
+    /**\r
+     * Method addJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJalviewModelSequence2Item\r
+     */\r
+    public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _items.insertElementAt(vJalviewModelSequence2Item, index);\r
+    } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
+\r
+    /**\r
+     * Method enumerateJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateJalviewModelSequence2Item()\r
+    {\r
+        return _items.elements();\r
+    } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() \r
+\r
+    /**\r
+     * Method getJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JalviewModelSequence2Item\r
+     */\r
+    public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _items.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
+    } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) \r
+\r
+    /**\r
+     * Method getJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @return JalviewModelSequence2Item\r
+     */\r
+    public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
+    {\r
+        int size = _items.size();\r
+        jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() \r
+\r
+    /**\r
+     * Method getJalviewModelSequence2ItemCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getJalviewModelSequence2ItemCount()\r
+    {\r
+        return _items.size();\r
+    } //-- int getJalviewModelSequence2ItemCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllJalviewModelSequence2Item\r
+     * \r
+     */\r
+    public void removeAllJalviewModelSequence2Item()\r
+    {\r
+        _items.removeAllElements();\r
+    } //-- void removeAllJalviewModelSequence2Item() \r
+\r
+    /**\r
+     * Method removeJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JalviewModelSequence2Item\r
+     */\r
+    public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int index)\r
+    {\r
+        java.lang.Object obj = _items.elementAt(index);\r
+        _items.removeElementAt(index);\r
+        return (jalview.binding.JalviewModelSequence2Item) obj;\r
+    } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) \r
+\r
+    /**\r
+     * Method setJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJalviewModelSequence2Item\r
+     */\r
+    public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _items.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _items.setElementAt(vJalviewModelSequence2Item, index);\r
+    } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
+\r
+    /**\r
+     * Method setJalviewModelSequence2Item\r
+     * \r
+     * \r
+     * \r
+     * @param jalviewModelSequence2ItemArray\r
+     */\r
+    public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)\r
+    {\r
+        //-- copy array\r
+        _items.removeAllElements();\r
+        for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {\r
+            _items.addElement(jalviewModelSequence2ItemArray[i]);\r
+        }\r
+    } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/JalviewModelSequence2Item.java b/src/jalview/binding/JalviewModelSequence2Item.java
new file mode 100755 (executable)
index 0000000..8678b09
--- /dev/null
+++ b/src/jalview/binding/JalviewModelSequence2Item.java
@@ -0,0 +1,197 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.Serializable;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class JalviewModelSequence2Item.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewModelSequence2Item implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _userColourSchemeList\r
+     */\r
+    private java.util.Vector _userColourSchemeList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModelSequence2Item() {\r
+        super();\r
+        _userColourSchemeList = new Vector();\r
+    } //-- jalview.binding.JalviewModelSequence2Item()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param vUserColourScheme\r
+     */\r
+    public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColourSchemeList.addElement(vUserColourScheme);\r
+    } //-- void addUserColourScheme(jalview.binding.UserColourScheme) \r
+\r
+    /**\r
+     * Method addUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColourScheme\r
+     */\r
+    public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColourSchemeList.insertElementAt(vUserColourScheme, index);\r
+    } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) \r
+\r
+    /**\r
+     * Method enumerateUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateUserColourScheme()\r
+    {\r
+        return _userColourSchemeList.elements();\r
+    } //-- java.util.Enumeration enumerateUserColourScheme() \r
+\r
+    /**\r
+     * Method getUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColourScheme\r
+     */\r
+    public jalview.binding.UserColourScheme getUserColourScheme(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColourSchemeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
+    } //-- jalview.binding.UserColourScheme getUserColourScheme(int) \r
+\r
+    /**\r
+     * Method getUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @return UserColourScheme\r
+     */\r
+    public jalview.binding.UserColourScheme[] getUserColourScheme()\r
+    {\r
+        int size = _userColourSchemeList.size();\r
+        jalview.binding.UserColourScheme[] mArray = new jalview.binding.UserColourScheme[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.UserColourScheme[] getUserColourScheme() \r
+\r
+    /**\r
+     * Method getUserColourSchemeCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getUserColourSchemeCount()\r
+    {\r
+        return _userColourSchemeList.size();\r
+    } //-- int getUserColourSchemeCount() \r
+\r
+    /**\r
+     * Method removeAllUserColourScheme\r
+     * \r
+     */\r
+    public void removeAllUserColourScheme()\r
+    {\r
+        _userColourSchemeList.removeAllElements();\r
+    } //-- void removeAllUserColourScheme() \r
+\r
+    /**\r
+     * Method removeUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColourScheme\r
+     */\r
+    public jalview.binding.UserColourScheme removeUserColourScheme(int index)\r
+    {\r
+        java.lang.Object obj = _userColourSchemeList.elementAt(index);\r
+        _userColourSchemeList.removeElementAt(index);\r
+        return (jalview.binding.UserColourScheme) obj;\r
+    } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) \r
+\r
+    /**\r
+     * Method setUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColourScheme\r
+     */\r
+    public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColourSchemeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _userColourSchemeList.setElementAt(vUserColourScheme, index);\r
+    } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) \r
+\r
+    /**\r
+     * Method setUserColourScheme\r
+     * \r
+     * \r
+     * \r
+     * @param userColourSchemeArray\r
+     */\r
+    public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)\r
+    {\r
+        //-- copy array\r
+        _userColourSchemeList.removeAllElements();\r
+        for (int i = 0; i < userColourSchemeArray.length; i++) {\r
+            _userColourSchemeList.addElement(userColourSchemeArray[i]);\r
+        }\r
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+\r
+}\r

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 (executable)
--- a/src/jalview/binding/JalviewState.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -15,7 +15,6 @@ import java.io.IOException;
 import java.io.Reader;\r
 import java.io.Serializable;\r
 import java.io.Writer;\r
-import java.util.Date;\r
 import java.util.Enumeration;\r
 import java.util.Vector;\r
 import org.exolab.castor.xml.MarshalException;\r
@@ -25,11 +24,11 @@ import org.exolab.castor.xml.ValidationException;
 import org.xml.sax.ContentHandler;\r
 \r
 /**\r
- * Class JalviewState.\r
+ * Class JalviewUserColours.\r
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewState implements java.io.Serializable {\r
+public class JalviewUserColours implements java.io.Serializable {\r
 \r
 \r
       //--------------------------/\r
@@ -37,24 +36,19 @@ public class JalviewState implements java.io.Serializable {
     //--------------------------/\r
 \r
     /**\r
-     * Field _creationDate\r
+     * Field _colourList\r
      */\r
-    private java.util.Date _creationDate;\r
-\r
-    /**\r
-     * Field _fileList\r
-     */\r
-    private java.util.Vector _fileList;\r
+    private java.util.Vector _colourList;\r
 \r
 \r
       //----------------/\r
      //- Constructors -/\r
     //----------------/\r
 \r
-    public JalviewState() {\r
+    public JalviewUserColours() {\r
         super();\r
-        _fileList = new Vector();\r
-    } //-- jalview.binding.JalviewState()\r
+        _colourList = new Vector();\r
+    } //-- jalview.binding.JalviewUserColours()\r
 \r
 \r
       //-----------/\r
@@ -62,102 +56,91 @@ public class JalviewState implements java.io.Serializable {
     //-----------/\r
 \r
     /**\r
-     * Method addFile\r
+     * Method addColour\r
      * \r
      * \r
      * \r
-     * @param vFile\r
+     * @param vColour\r
      */\r
-    public void addFile(java.lang.String vFile)\r
+    public void addColour(jalview.binding.Colour vColour)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
-        _fileList.addElement(vFile);\r
-    } //-- void addFile(java.lang.String) \r
+        _colourList.addElement(vColour);\r
+    } //-- void addColour(jalview.binding.Colour) \r
 \r
     /**\r
-     * Method addFile\r
+     * Method addColour\r
      * \r
      * \r
      * \r
      * @param index\r
-     * @param vFile\r
+     * @param vColour\r
      */\r
-    public void addFile(int index, java.lang.String vFile)\r
+    public void addColour(int index, jalview.binding.Colour vColour)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
-        _fileList.insertElementAt(vFile, index);\r
-    } //-- void addFile(int, java.lang.String) \r
+        _colourList.insertElementAt(vColour, index);\r
+    } //-- void addColour(int, jalview.binding.Colour) \r
 \r
     /**\r
-     * Method enumerateFile\r
+     * Method enumerateColour\r
      * \r
      * \r
      * \r
      * @return Enumeration\r
      */\r
-    public java.util.Enumeration enumerateFile()\r
+    public java.util.Enumeration enumerateColour()\r
     {\r
-        return _fileList.elements();\r
-    } //-- java.util.Enumeration enumerateFile() \r
+        return _colourList.elements();\r
+    } //-- java.util.Enumeration enumerateColour() \r
 \r
     /**\r
-     * Returns the value of field 'creationDate'.\r
-     * \r
-     * @return Date\r
-     * @return the value of field 'creationDate'.\r
-     */\r
-    public java.util.Date getCreationDate()\r
-    {\r
-        return this._creationDate;\r
-    } //-- java.util.Date getCreationDate() \r
-\r
-    /**\r
-     * Method getFile\r
+     * Method getColour\r
      * \r
      * \r
      * \r
      * @param index\r
-     * @return String\r
+     * @return Colour\r
      */\r
-    public java.lang.String getFile(int index)\r
+    public jalview.binding.Colour getColour(int index)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
-        if ((index < 0) || (index > _fileList.size())) {\r
+        if ((index < 0) || (index > _colourList.size())) {\r
             throw new IndexOutOfBoundsException();\r
         }\r
         \r
-        return (String)_fileList.elementAt(index);\r
-    } //-- java.lang.String getFile(int) \r
+        return (jalview.binding.Colour) _colourList.elementAt(index);\r
+    } //-- jalview.binding.Colour getColour(int) \r
 \r
     /**\r
-     * Method getFile\r
+     * Method getColour\r
      * \r
      * \r
      * \r
-     * @return String\r
+     * @return Colour\r
      */\r
-    public java.lang.String[] getFile()\r
+    public jalview.binding.Colour[] getColour()\r
     {\r
-        int size = _fileList.size();\r
-        java.lang.String[] mArray = new java.lang.String[size];\r
+        int size = _colourList.size();\r
+        jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];\r
         for (int index = 0; index < size; index++) {\r
-            mArray[index] = (String)_fileList.elementAt(index);\r
+            mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
         }\r
         return mArray;\r
-    } //-- java.lang.String[] getFile() \r
+    } //-- jalview.binding.Colour[] getColour() \r
 \r
     /**\r
-     * Method getFileCount\r
+     * Method getColourCount\r
      * \r
      * \r
      * \r
      * @return int\r
      */\r
-    public int getFileCount()\r
+    public int getColourCount()\r
     {\r
-        return _fileList.size();\r
-    } //-- int getFileCount() \r
+        return _colourList.size();\r
+    } //-- int getColourCount() \r
 \r
     /**\r
      * Method isValid\r
@@ -206,72 +189,62 @@ public class JalviewState implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
     /**\r
-     * Method removeAllFile\r
+     * Method removeAllColour\r
      * \r
      */\r
-    public void removeAllFile()\r
+    public void removeAllColour()\r
     {\r
-        _fileList.removeAllElements();\r
-    } //-- void removeAllFile() \r
+        _colourList.removeAllElements();\r
+    } //-- void removeAllColour() \r
 \r
     /**\r
-     * Method removeFile\r
+     * Method removeColour\r
      * \r
      * \r
      * \r
      * @param index\r
-     * @return String\r
-     */\r
-    public java.lang.String removeFile(int index)\r
-    {\r
-        java.lang.Object obj = _fileList.elementAt(index);\r
-        _fileList.removeElementAt(index);\r
-        return (String)obj;\r
-    } //-- java.lang.String removeFile(int) \r
-\r
-    /**\r
-     * Sets the value of field 'creationDate'.\r
-     * \r
-     * @param creationDate the value of field 'creationDate'.\r
+     * @return Colour\r
      */\r
-    public void setCreationDate(java.util.Date creationDate)\r
+    public jalview.binding.Colour removeColour(int index)\r
     {\r
-        this._creationDate = creationDate;\r
-    } //-- void setCreationDate(java.util.Date) \r
+        java.lang.Object obj = _colourList.elementAt(index);\r
+        _colourList.removeElementAt(index);\r
+        return (jalview.binding.Colour) obj;\r
+    } //-- jalview.binding.Colour removeColour(int) \r
 \r
     /**\r
-     * Method setFile\r
+     * Method setColour\r
      * \r
      * \r
      * \r
      * @param index\r
-     * @param vFile\r
+     * @param vColour\r
      */\r
-    public void setFile(int index, java.lang.String vFile)\r
+    public void setColour(int index, jalview.binding.Colour vColour)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
-        if ((index < 0) || (index > _fileList.size())) {\r
+        if ((index < 0) || (index > _colourList.size())) {\r
             throw new IndexOutOfBoundsException();\r
         }\r
-        _fileList.setElementAt(vFile, index);\r
-    } //-- void setFile(int, java.lang.String) \r
+        _colourList.setElementAt(vColour, index);\r
+    } //-- void setColour(int, jalview.binding.Colour) \r
 \r
     /**\r
-     * Method setFile\r
+     * Method setColour\r
      * \r
      * \r
      * \r
-     * @param fileArray\r
+     * @param colourArray\r
      */\r
-    public void setFile(java.lang.String[] fileArray)\r
+    public void setColour(jalview.binding.Colour[] colourArray)\r
     {\r
         //-- copy array\r
-        _fileList.removeAllElements();\r
-        for (int i = 0; i < fileArray.length; i++) {\r
-            _fileList.addElement(fileArray[i]);\r
+        _colourList.removeAllElements();\r
+        for (int i = 0; i < colourArray.length; i++) {\r
+            _colourList.addElement(colourArray[i]);\r
         }\r
-    } //-- void setFile(java.lang.String) \r
+    } //-- void setColour(jalview.binding.Colour) \r
 \r
     /**\r
      * Method unmarshal\r
@@ -284,7 +257,7 @@ public class JalviewState implements java.io.Serializable {
     public static java.lang.Object unmarshal(java.io.Reader reader)\r
         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-        return (jalview.binding.JalviewState) Unmarshaller.unmarshal(jalview.binding.JalviewState.class, reader);\r
+        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);\r
     } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r

diff --git a/src/jalview/binding/JalviewUserColoursItem.java b/src/jalview/binding/JalviewUserColoursItem.java
new file mode 100755 (executable)
index 0000000..ce6919c
--- /dev/null
+++ b/src/jalview/binding/JalviewUserColoursItem.java
@@ -0,0 +1,70 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.Serializable;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class JalviewUserColoursItem.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class JalviewUserColoursItem implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private jalview.binding.Colour _colour;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewUserColoursItem() {\r
+        super();\r
+    } //-- jalview.binding.JalviewUserColoursItem()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return Colour\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public jalview.binding.Colour getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- jalview.binding.Colour getColour() \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(jalview.binding.Colour colour)\r
+    {\r
+        this._colour = colour;\r
+    } //-- void setColour(jalview.binding.Colour) \r
+\r
+}\r

diff --git a/src/jalview/binding/Residue.java b/src/jalview/binding/Residue.java
new file mode 100755 (executable)
index 0000000..69e4312
--- /dev/null
+++ b/src/jalview/binding/Residue.java
@@ -0,0 +1,200 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Residue.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Residue implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+    /**\r
+     * Field _RGB\r
+     */\r
+    private int _RGB;\r
+\r
+    /**\r
+     * keeps track of state for field: _RGB\r
+     */\r
+    private boolean _has_RGB;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Residue() {\r
+        super();\r
+    } //-- jalview.binding.Residue()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteRGB\r
+     * \r
+     */\r
+    public void deleteRGB()\r
+    {\r
+        this._has_RGB= false;\r
+    } //-- void deleteRGB() \r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'RGB'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'RGB'.\r
+     */\r
+    public int getRGB()\r
+    {\r
+        return this._RGB;\r
+    } //-- int getRGB() \r
+\r
+    /**\r
+     * Method hasRGB\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasRGB()\r
+    {\r
+        return this._has_RGB;\r
+    } //-- boolean hasRGB() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'RGB'.\r
+     * \r
+     * @param RGB the value of field 'RGB'.\r
+     */\r
+    public void setRGB(int RGB)\r
+    {\r
+        this._RGB = RGB;\r
+        this._has_RGB = true;\r
+    } //-- void setRGB(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/UserColour.java b/src/jalview/binding/UserColour.java
new file mode 100755 (executable)
index 0000000..837d9af
--- /dev/null
+++ b/src/jalview/binding/UserColour.java
@@ -0,0 +1,200 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class UserColour.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class UserColour implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private int _id;\r
+\r
+    /**\r
+     * keeps track of state for field: _id\r
+     */\r
+    private boolean _has_id;\r
+\r
+    /**\r
+     * Field _userColourScheme\r
+     */\r
+    private jalview.binding.UserColourScheme _userColourScheme;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColour() {\r
+        super();\r
+    } //-- jalview.binding.UserColour()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteId\r
+     * \r
+     */\r
+    public void deleteId()\r
+    {\r
+        this._has_id= false;\r
+    } //-- void deleteId() \r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'id'.\r
+     */\r
+    public int getId()\r
+    {\r
+        return this._id;\r
+    } //-- int getId() \r
+\r
+    /**\r
+     * Returns the value of field 'userColourScheme'.\r
+     * \r
+     * @return UserColourScheme\r
+     * @return the value of field 'userColourScheme'.\r
+     */\r
+    public jalview.binding.UserColourScheme getUserColourScheme()\r
+    {\r
+        return this._userColourScheme;\r
+    } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
+\r
+    /**\r
+     * Method hasId\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasId()\r
+    {\r
+        return this._has_id;\r
+    } //-- boolean hasId() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(int id)\r
+    {\r
+        this._id = id;\r
+        this._has_id = true;\r
+    } //-- void setId(int) \r
+\r
+    /**\r
+     * Sets the value of field 'userColourScheme'.\r
+     * \r
+     * @param userColourScheme the value of field 'userColourScheme'\r
+     */\r
+    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
+    {\r
+        this._userColourScheme = userColourScheme;\r
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
new file mode 100755 (executable)
index 0000000..79ea637
--- /dev/null
+++ b/src/jalview/binding/UserColourScheme.java
@@ -0,0 +1,118 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class UserColourScheme.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class UserColourScheme extends JalviewUserColours \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColourScheme() {\r
+        super();\r
+    } //-- jalview.binding.UserColourScheme()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
new file mode 100755 (executable)
index 0000000..241aaab
--- /dev/null
+++ b/src/jalview/binding/UserColours.java
@@ -0,0 +1,173 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class UserColours.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class UserColours implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _userColourScheme\r
+     */\r
+    private jalview.binding.UserColourScheme _userColourScheme;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColours() {\r
+        super();\r
+    } //-- jalview.binding.UserColours()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'id'.\r
+     */\r
+    public java.lang.String getId()\r
+    {\r
+        return this._id;\r
+    } //-- java.lang.String getId() \r
+\r
+    /**\r
+     * Returns the value of field 'userColourScheme'.\r
+     * \r
+     * @return UserColourScheme\r
+     * @return the value of field 'userColourScheme'.\r
+     */\r
+    public jalview.binding.UserColourScheme getUserColourScheme()\r
+    {\r
+        return this._userColourScheme;\r
+    } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(java.lang.String id)\r
+    {\r
+        this._id = id;\r
+    } //-- void setId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'userColourScheme'.\r
+     * \r
+     * @param userColourScheme the value of field 'userColourScheme'\r
+     */\r
+    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
+    {\r
+        this._userColourScheme = userColourScheme;\r
+    } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r