JAL-1397 store colour by sequence and originalColour flags for AnnotationColourScheme
authorJim Procter <jprocter@compbio.dundee.ac.uk>
Thu, 17 Oct 2013 10:13:02 +0000 (11:13 +0100)
committerJim Procter <jprocter@compbio.dundee.ac.uk>
Thu, 17 Oct 2013 10:14:09 +0000 (11:14 +0100)
schemas/jalview.xsd
src/jalview/gui/Jalview2XML.java
src/jalview/schemabinding/version2/.castor.cdr
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java

index 03c5728..0138f63 100755 (executable)
                                                                                type="xs:string" />
                                                                        <xs:attribute name="threshold"
                                                                                type="xs:float" />
+                       <xs:attribute name="perSequence" 
+                       type="xs:boolean" 
+                       use="optional" />
+                       <xs:attribute name="predefinedColours" 
+                  type="xs:boolean" 
+                  use="optional" />
                                                                </xs:complexType>
                                                        </xs:element>
                                                        <xs:element name="hiddenColumns"
index 2ec76a7..0a0b169 100644 (file)
@@ -1069,6 +1069,8 @@ public class Jalview2XML
 
       ac.setMaxColour(acg.getMaxColour().getRGB());
       ac.setMinColour(acg.getMinColour().getRGB());
+      ac.setPerSequence(acg.isSeqAssociated());
+      ac.setPredefinedColours(acg.isPredefinedColours());
       view.setAnnotationColours(ac);
       view.setBgColour("AnnotationColourGradient");
     }
@@ -3238,7 +3240,14 @@ public class Jalview2XML
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
               }
-
+              if (view.getAnnotationColours().hasPerSequence())
+              {
+                ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+              }
+              if (view.getAnnotationColours().hasPredefinedColours())
+              {
+                ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+              }
               // Also use these settings for all the groups
               if (al.getGroups() != null)
               {
@@ -3268,6 +3277,17 @@ public class Jalview2XML
                             .getAlignment().getAlignmentAnnotation()[i],
                             sg.cs, view.getAnnotationColours()
                                     .getAboveThreshold());
+                    if (cs instanceof AnnotationColourGradient) 
+                    {
+                      if (view.getAnnotationColours().hasPerSequence())
+                      { 
+                        ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
+                      }
+                      if (view.getAnnotationColours().hasPredefinedColours())
+                      {
+                        ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
+                      }
+                    }
                   }
 
                 }
index abf5fc6..af45e9d 100644 (file)
@@ -1,4 +1,4 @@
-#Thu Sep 06 17:55:29 BST 2012
+#Thu Oct 17 10:35:33 BST 2013
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
index 805e70c..9eef6f0 100644 (file)
@@ -1,24 +1,14 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -29,360 +19,461 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColours implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _aboveThreshold.
-   */
-  private int _aboveThreshold;
-
-  /**
-   * keeps track of state for field: _aboveThreshold
-   */
-  private boolean _has_aboveThreshold;
-
-  /**
-   * Field _annotation.
-   */
-  private java.lang.String _annotation;
-
-  /**
-   * Field _minColour.
-   */
-  private int _minColour;
-
-  /**
-   * keeps track of state for field: _minColour
-   */
-  private boolean _has_minColour;
-
-  /**
-   * Field _maxColour.
-   */
-  private int _maxColour;
-
-  /**
-   * keeps track of state for field: _maxColour
-   */
-  private boolean _has_maxColour;
-
-  /**
-   * Field _colourScheme.
-   */
-  private java.lang.String _colourScheme;
-
-  /**
-   * Field _threshold.
-   */
-  private float _threshold;
-
-  /**
-   * keeps track of state for field: _threshold
-   */
-  private boolean _has_threshold;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public AnnotationColours()
-  {
-    super();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-     */
-  public void deleteAboveThreshold()
-  {
-    this._has_aboveThreshold = false;
-  }
-
-  /**
-     */
-  public void deleteMaxColour()
-  {
-    this._has_maxColour = false;
-  }
-
-  /**
-     */
-  public void deleteMinColour()
-  {
-    this._has_minColour = false;
-  }
-
-  /**
-     */
-  public void deleteThreshold()
-  {
-    this._has_threshold = false;
-  }
-
-  /**
-   * Returns the value of field 'aboveThreshold'.
-   * 
-   * @return the value of field 'AboveThreshold'.
-   */
-  public int getAboveThreshold()
-  {
-    return this._aboveThreshold;
-  }
-
-  /**
-   * Returns the value of field 'annotation'.
-   * 
-   * @return the value of field 'Annotation'.
-   */
-  public java.lang.String getAnnotation()
-  {
-    return this._annotation;
-  }
-
-  /**
-   * Returns the value of field 'colourScheme'.
-   * 
-   * @return the value of field 'ColourScheme'.
-   */
-  public java.lang.String getColourScheme()
-  {
-    return this._colourScheme;
-  }
-
-  /**
-   * Returns the value of field 'maxColour'.
-   * 
-   * @return the value of field 'MaxColour'.
-   */
-  public int getMaxColour()
-  {
-    return this._maxColour;
-  }
-
-  /**
-   * Returns the value of field 'minColour'.
-   * 
-   * @return the value of field 'MinColour'.
-   */
-  public int getMinColour()
-  {
-    return this._minColour;
-  }
-
-  /**
-   * Returns the value of field 'threshold'.
-   * 
-   * @return the value of field 'Threshold'.
-   */
-  public float getThreshold()
-  {
-    return this._threshold;
-  }
-
-  /**
-   * Method hasAboveThreshold.
-   * 
-   * @return true if at least one AboveThreshold has been added
-   */
-  public boolean hasAboveThreshold()
-  {
-    return this._has_aboveThreshold;
-  }
-
-  /**
-   * Method hasMaxColour.
-   * 
-   * @return true if at least one MaxColour has been added
-   */
-  public boolean hasMaxColour()
-  {
-    return this._has_maxColour;
-  }
-
-  /**
-   * Method hasMinColour.
-   * 
-   * @return true if at least one MinColour has been added
-   */
-  public boolean hasMinColour()
-  {
-    return this._has_minColour;
-  }
-
-  /**
-   * Method hasThreshold.
-   * 
-   * @return true if at least one Threshold has been added
-   */
-  public boolean hasThreshold()
-  {
-    return this._has_threshold;
-  }
-
-  /**
-   * Method isValid.
-   * 
-   * @return true if this object is valid according to the schema
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    } catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  }
-
-  /**
-   * 
-   * 
-   * @param out
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void marshal(final java.io.Writer out)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, out);
-  }
-
-  /**
-   * 
-   * 
-   * @param handler
-   * @throws java.io.IOException
-   *           if an IOException occurs during marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   */
-  public void marshal(final org.xml.sax.ContentHandler handler)
-          throws java.io.IOException,
-          org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, handler);
-  }
-
-  /**
-   * Sets the value of field 'aboveThreshold'.
-   * 
-   * @param aboveThreshold
-   *          the value of field 'aboveThreshold'.
-   */
-  public void setAboveThreshold(final int aboveThreshold)
-  {
-    this._aboveThreshold = aboveThreshold;
-    this._has_aboveThreshold = true;
-  }
-
-  /**
-   * Sets the value of field 'annotation'.
-   * 
-   * @param annotation
-   *          the value of field 'annotation'.
-   */
-  public void setAnnotation(final java.lang.String annotation)
-  {
-    this._annotation = annotation;
-  }
-
-  /**
-   * Sets the value of field 'colourScheme'.
-   * 
-   * @param colourScheme
-   *          the value of field 'colourScheme'.
-   */
-  public void setColourScheme(final java.lang.String colourScheme)
-  {
-    this._colourScheme = colourScheme;
-  }
-
-  /**
-   * Sets the value of field 'maxColour'.
-   * 
-   * @param maxColour
-   *          the value of field 'maxColour'.
-   */
-  public void setMaxColour(final int maxColour)
-  {
-    this._maxColour = maxColour;
-    this._has_maxColour = true;
-  }
-
-  /**
-   * Sets the value of field 'minColour'.
-   * 
-   * @param minColour
-   *          the value of field 'minColour'.
-   */
-  public void setMinColour(final int minColour)
-  {
-    this._minColour = minColour;
-    this._has_minColour = true;
-  }
-
-  /**
-   * Sets the value of field 'threshold'.
-   * 
-   * @param threshold
-   *          the value of field 'threshold'.
-   */
-  public void setThreshold(final float threshold)
-  {
-    this._threshold = threshold;
-    this._has_threshold = true;
-  }
-
-  /**
-   * Method unmarshal.
-   * 
-   * @param reader
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @return the unmarshaled jalview.schemabinding.version2.AnnotationColours
-   */
-  public static jalview.schemabinding.version2.AnnotationColours unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller
-            .unmarshal(
-                    jalview.schemabinding.version2.AnnotationColours.class,
-                    reader);
-  }
-
-  /**
-   * 
-   * 
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void validate() throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-    validator.validate(this);
-  }
+public class AnnotationColours implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _aboveThreshold.
+     */
+    private int _aboveThreshold;
+
+    /**
+     * keeps track of state for field: _aboveThreshold
+     */
+    private boolean _has_aboveThreshold;
+
+    /**
+     * Field _annotation.
+     */
+    private java.lang.String _annotation;
+
+    /**
+     * Field _minColour.
+     */
+    private int _minColour;
+
+    /**
+     * keeps track of state for field: _minColour
+     */
+    private boolean _has_minColour;
+
+    /**
+     * Field _maxColour.
+     */
+    private int _maxColour;
+
+    /**
+     * keeps track of state for field: _maxColour
+     */
+    private boolean _has_maxColour;
+
+    /**
+     * Field _colourScheme.
+     */
+    private java.lang.String _colourScheme;
+
+    /**
+     * Field _threshold.
+     */
+    private float _threshold;
+
+    /**
+     * keeps track of state for field: _threshold
+     */
+    private boolean _has_threshold;
+
+    /**
+     * Field _perSequence.
+     */
+    private boolean _perSequence;
+
+    /**
+     * keeps track of state for field: _perSequence
+     */
+    private boolean _has_perSequence;
+
+    /**
+     * Field _predefinedColours.
+     */
+    private boolean _predefinedColours;
+
+    /**
+     * keeps track of state for field: _predefinedColours
+     */
+    private boolean _has_predefinedColours;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationColours() {
+        super();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     */
+    public void deleteAboveThreshold(
+    ) {
+        this._has_aboveThreshold= false;
+    }
+
+    /**
+     */
+    public void deleteMaxColour(
+    ) {
+        this._has_maxColour= false;
+    }
+
+    /**
+     */
+    public void deleteMinColour(
+    ) {
+        this._has_minColour= false;
+    }
+
+    /**
+     */
+    public void deletePerSequence(
+    ) {
+        this._has_perSequence= false;
+    }
+
+    /**
+     */
+    public void deletePredefinedColours(
+    ) {
+        this._has_predefinedColours= false;
+    }
+
+    /**
+     */
+    public void deleteThreshold(
+    ) {
+        this._has_threshold= false;
+    }
+
+    /**
+     * Returns the value of field 'aboveThreshold'.
+     * 
+     * @return the value of field 'AboveThreshold'.
+     */
+    public int getAboveThreshold(
+    ) {
+        return this._aboveThreshold;
+    }
+
+    /**
+     * Returns the value of field 'annotation'.
+     * 
+     * @return the value of field 'Annotation'.
+     */
+    public java.lang.String getAnnotation(
+    ) {
+        return this._annotation;
+    }
+
+    /**
+     * Returns the value of field 'colourScheme'.
+     * 
+     * @return the value of field 'ColourScheme'.
+     */
+    public java.lang.String getColourScheme(
+    ) {
+        return this._colourScheme;
+    }
+
+    /**
+     * Returns the value of field 'maxColour'.
+     * 
+     * @return the value of field 'MaxColour'.
+     */
+    public int getMaxColour(
+    ) {
+        return this._maxColour;
+    }
+
+    /**
+     * Returns the value of field 'minColour'.
+     * 
+     * @return the value of field 'MinColour'.
+     */
+    public int getMinColour(
+    ) {
+        return this._minColour;
+    }
+
+    /**
+     * Returns the value of field 'perSequence'.
+     * 
+     * @return the value of field 'PerSequence'.
+     */
+    public boolean getPerSequence(
+    ) {
+        return this._perSequence;
+    }
+
+    /**
+     * Returns the value of field 'predefinedColours'.
+     * 
+     * @return the value of field 'PredefinedColours'.
+     */
+    public boolean getPredefinedColours(
+    ) {
+        return this._predefinedColours;
+    }
+
+    /**
+     * Returns the value of field 'threshold'.
+     * 
+     * @return the value of field 'Threshold'.
+     */
+    public float getThreshold(
+    ) {
+        return this._threshold;
+    }
+
+    /**
+     * Method hasAboveThreshold.
+     * 
+     * @return true if at least one AboveThreshold has been added
+     */
+    public boolean hasAboveThreshold(
+    ) {
+        return this._has_aboveThreshold;
+    }
+
+    /**
+     * Method hasMaxColour.
+     * 
+     * @return true if at least one MaxColour has been added
+     */
+    public boolean hasMaxColour(
+    ) {
+        return this._has_maxColour;
+    }
+
+    /**
+     * Method hasMinColour.
+     * 
+     * @return true if at least one MinColour has been added
+     */
+    public boolean hasMinColour(
+    ) {
+        return this._has_minColour;
+    }
+
+    /**
+     * Method hasPerSequence.
+     * 
+     * @return true if at least one PerSequence has been added
+     */
+    public boolean hasPerSequence(
+    ) {
+        return this._has_perSequence;
+    }
+
+    /**
+     * Method hasPredefinedColours.
+     * 
+     * @return true if at least one PredefinedColours has been added
+     */
+    public boolean hasPredefinedColours(
+    ) {
+        return this._has_predefinedColours;
+    }
+
+    /**
+     * Method hasThreshold.
+     * 
+     * @return true if at least one Threshold has been added
+     */
+    public boolean hasThreshold(
+    ) {
+        return this._has_threshold;
+    }
+
+    /**
+     * Returns the value of field 'perSequence'.
+     * 
+     * @return the value of field 'PerSequence'.
+     */
+    public boolean isPerSequence(
+    ) {
+        return this._perSequence;
+    }
+
+    /**
+     * Returns the value of field 'predefinedColours'.
+     * 
+     * @return the value of field 'PredefinedColours'.
+     */
+    public boolean isPredefinedColours(
+    ) {
+        return this._predefinedColours;
+    }
+
+    /**
+     * Method isValid.
+     * 
+     * @return true if this object is valid according to the schema
+     */
+    public boolean isValid(
+    ) {
+        try {
+            validate();
+        } catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * 
+     * 
+     * @param out
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, out);
+    }
+
+    /**
+     * 
+     * 
+     * @param handler
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, handler);
+    }
+
+    /**
+     * Sets the value of field 'aboveThreshold'.
+     * 
+     * @param aboveThreshold the value of field 'aboveThreshold'.
+     */
+    public void setAboveThreshold(
+            final int aboveThreshold) {
+        this._aboveThreshold = aboveThreshold;
+        this._has_aboveThreshold = true;
+    }
+
+    /**
+     * Sets the value of field 'annotation'.
+     * 
+     * @param annotation the value of field 'annotation'.
+     */
+    public void setAnnotation(
+            final java.lang.String annotation) {
+        this._annotation = annotation;
+    }
+
+    /**
+     * Sets the value of field 'colourScheme'.
+     * 
+     * @param colourScheme the value of field 'colourScheme'.
+     */
+    public void setColourScheme(
+            final java.lang.String colourScheme) {
+        this._colourScheme = colourScheme;
+    }
+
+    /**
+     * Sets the value of field 'maxColour'.
+     * 
+     * @param maxColour the value of field 'maxColour'.
+     */
+    public void setMaxColour(
+            final int maxColour) {
+        this._maxColour = maxColour;
+        this._has_maxColour = true;
+    }
+
+    /**
+     * Sets the value of field 'minColour'.
+     * 
+     * @param minColour the value of field 'minColour'.
+     */
+    public void setMinColour(
+            final int minColour) {
+        this._minColour = minColour;
+        this._has_minColour = true;
+    }
+
+    /**
+     * Sets the value of field 'perSequence'.
+     * 
+     * @param perSequence the value of field 'perSequence'.
+     */
+    public void setPerSequence(
+            final boolean perSequence) {
+        this._perSequence = perSequence;
+        this._has_perSequence = true;
+    }
+
+    /**
+     * Sets the value of field 'predefinedColours'.
+     * 
+     * @param predefinedColours the value of field
+     * 'predefinedColours'.
+     */
+    public void setPredefinedColours(
+            final boolean predefinedColours) {
+        this._predefinedColours = predefinedColours;
+        this._has_predefinedColours = true;
+    }
+
+    /**
+     * Sets the value of field 'threshold'.
+     * 
+     * @param threshold the value of field 'threshold'.
+     */
+    public void setThreshold(
+            final float threshold) {
+        this._threshold = threshold;
+        this._has_threshold = true;
+    }
+
+    /**
+     * Method unmarshal.
+     * 
+     * @param reader
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled
+     * jalview.schemabinding.version2.AnnotationColours
+     */
+    public static jalview.schemabinding.version2.AnnotationColours unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
+    }
+
+    /**
+     * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    }
 
 }
index 876e928..196ad60 100644 (file)
@@ -1,24 +1,14 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.schemabinding.version2.descriptors;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.AnnotationColours;
@@ -28,447 +18,468 @@ import jalview.schemabinding.version2.AnnotationColours;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColoursDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _elementDefinition.
-   */
-  private boolean _elementDefinition;
-
-  /**
-   * Field _nsPrefix.
-   */
-  private java.lang.String _nsPrefix;
-
-  /**
-   * Field _nsURI.
-   */
-  private java.lang.String _nsURI;
-
-  /**
-   * Field _xmlName.
-   */
-  private java.lang.String _xmlName;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public AnnotationColoursDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "AnnotationColours";
-    _elementDefinition = true;
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
-    org.exolab.castor.mapping.FieldHandler handler = null;
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;
-    // -- initialize attribute descriptors
-
-    // -- _aboveThreshold
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        if (!target.hasAboveThreshold())
-        {
-          return null;
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationColoursDescriptor() {
+        super();
+        _nsURI = "www.jalview.org";
+        _xmlName = "AnnotationColours";
+        _elementDefinition = true;
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _aboveThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasAboveThreshold()) { return null; }
+                return new java.lang.Integer(target.getAboveThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteAboveThreshold();
+                        return;
+                    }
+                    target.setAboveThreshold( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _aboveThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-        return new java.lang.Integer(target.getAboveThreshold());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteAboveThreshold();
-            return;
-          }
-          target.setAboveThreshold(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _annotation
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                return target.getAnnotation();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    target.setAnnotation( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotation
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _aboveThreshold
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _annotation
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_annotation", "annotation",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        return target.getAnnotation();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          target.setAnnotation((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _minColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasMinColour()) { return null; }
+                return new java.lang.Integer(target.getMinColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteMinColour();
+                        return;
+                    }
+                    target.setMinColour( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _minColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _annotation
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
-    }
-    desc.setValidator(fieldValidator);
-    // -- _minColour
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_minColour", "minColour",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        if (!target.hasMinColour())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _maxColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasMaxColour()) { return null; }
+                return new java.lang.Integer(target.getMaxColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteMaxColour();
+                        return;
+                    }
+                    target.setMaxColour( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _maxColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-        return new java.lang.Integer(target.getMinColour());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteMinColour();
-            return;
-          }
-          target.setMinColour(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _colourScheme
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                return target.getColourScheme();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    target.setColourScheme( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colourScheme
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _minColour
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _maxColour
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_maxColour", "maxColour",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        if (!target.hasMaxColour())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _threshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasThreshold()) { return null; }
+                return new java.lang.Float(target.getThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteThreshold();
+                        return;
+                    }
+                    target.setThreshold( ((java.lang.Float) value).floatValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _threshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.FloatValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive((float) -3.4028235E38);
+            typeValidator.setMaxInclusive((float) 3.4028235E38);
         }
-        return new java.lang.Integer(target.getMaxColour());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteMaxColour();
-            return;
-          }
-          target.setMaxColour(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _perSequence
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasPerSequence()) { return null; }
+                return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deletePerSequence();
+                        return;
+                    }
+                    target.setPerSequence( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _perSequence
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _maxColour
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _colourScheme
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_colourScheme", "colourScheme",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        return target.getColourScheme();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          target.setColourScheme((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _predefinedColours
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if (!target.hasPredefinedColours()) { return null; }
+                return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deletePredefinedColours();
+                        return;
+                    }
+                    target.setPredefinedColours( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _predefinedColours
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _colourScheme
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
     }
-    desc.setValidator(fieldValidator);
-    // -- _threshold
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Float.TYPE, "_threshold", "threshold",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        AnnotationColours target = (AnnotationColours) object;
-        if (!target.hasThreshold())
-        {
-          return null;
-        }
-        return new java.lang.Float(target.getThreshold());
-      }
 
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          AnnotationColours target = (AnnotationColours) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteThreshold();
-            return;
-          }
-          target.setThreshold(((java.lang.Float) value).floatValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
+      //-----------/
+     //- Methods -/
+    //-----------/
 
-    // -- validation code for: _threshold
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.FloatValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive((float) -3.4028235E38);
-      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
+        return null;
     }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
-
-  }
 
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Method getAccessMode.
-   * 
-   * @return the access mode specified for this class.
-   */
-  public org.exolab.castor.mapping.AccessMode getAccessMode()
-  {
-    return null;
-  }
-
-  /**
-   * Method getIdentity.
-   * 
-   * @return the identity field, null if this class has no identity.
-   */
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-  {
-    return super.getIdentity();
-  }
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
+    }
 
-  /**
-   * Method getJavaClass.
-   * 
-   * @return the Java class represented by this descriptor.
-   */
-  public java.lang.Class getJavaClass()
-  {
-    return jalview.schemabinding.version2.AnnotationColours.class;
-  }
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.AnnotationColours.class;
+    }
 
-  /**
-   * Method getNameSpacePrefix.
-   * 
-   * @return the namespace prefix to use when marshaling as XML.
-   */
-  public java.lang.String getNameSpacePrefix()
-  {
-    return _nsPrefix;
-  }
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
+    }
 
-  /**
-   * Method getNameSpaceURI.
-   * 
-   * @return the namespace URI used when marshaling and unmarshaling as XML.
-   */
-  public java.lang.String getNameSpaceURI()
-  {
-    return _nsURI;
-  }
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
 
-  /**
-   * Method getValidator.
-   * 
-   * @return a specific validator for the class described by this
-   *         ClassDescriptor.
-   */
-  public org.exolab.castor.xml.TypeValidator getValidator()
-  {
-    return this;
-  }
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
 
-  /**
-   * Method getXMLName.
-   * 
-   * @return the XML Name for the Class being described.
-   */
-  public java.lang.String getXMLName()
-  {
-    return _xmlName;
-  }
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
 
-  /**
-   * Method isElementDefinition.
-   * 
-   * @return true if XML schema definition of this Class is that of a global
-   *         element or element with anonymous type definition.
-   */
-  public boolean isElementDefinition()
-  {
-    return _elementDefinition;
-  }
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
+    }
 
 }