X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=b7056c4214468152636898062e9e577e1d200188;hb=0233fbee0ff0d7fad302aa2da743c51fd64be101;hp=9eb69079eb0cb15a71f1314a49e325dd0829efec;hpb=6951479b7dc56bd022ce2c370b7f88b5571004fd;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 9eb6907..b7056c4 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,27 +1,29 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
   //---------------------------------/
  //- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
 
 /**
  * Class Annotation.
@@ -36,7 +38,7 @@ public class Annotation implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _graph
+     * Field _graph.
      */
     private boolean _graph;
 
@@ -46,7 +48,7 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_graph;
 
     /**
-     * Field _graphType
+     * Field _graphType.
      */
     private int _graphType;
 
@@ -56,12 +58,17 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_graphType;
 
     /**
-     * Field _sequenceRef
+     * Field _sequenceRef.
      */
     private java.lang.String _sequenceRef;
 
     /**
-     * Field _graphColour
+     * Field _groupRef.
+     */
+    private java.lang.String _groupRef;
+
+    /**
+     * Field _graphColour.
      */
     private int _graphColour;
 
@@ -71,7 +78,7 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_graphColour;
 
     /**
-     * Field _graphGroup
+     * Field _graphGroup.
      */
     private int _graphGroup;
 
@@ -81,12 +88,12 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_graphGroup;
 
     /**
-     * Field _id
+     * Field _id.
      */
     private java.lang.String _id;
 
     /**
-     * Field _scoreOnly
+     * Field _scoreOnly.
      */
     private boolean _scoreOnly = false;
 
@@ -96,9 +103,9 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_scoreOnly;
 
     /**
-     * Field _score
+     * Field _score.
      */
-    private float _score;
+    private double _score;
 
     /**
      * keeps track of state for field: _score
@@ -106,22 +113,72 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_score;
 
     /**
-     * Field _annotationElementList
+     * Field _visible.
+     */
+    private boolean _visible;
+
+    /**
+     * keeps track of state for field: _visible
+     */
+    private boolean _has_visible;
+
+    /**
+     * Field _centreColLabels.
+     */
+    private boolean _centreColLabels;
+
+    /**
+     * keeps track of state for field: _centreColLabels
+     */
+    private boolean _has_centreColLabels;
+
+    /**
+     * Field _scaleColLabels.
+     */
+    private boolean _scaleColLabels;
+
+    /**
+     * keeps track of state for field: _scaleColLabels
+     */
+    private boolean _has_scaleColLabels;
+
+    /**
+     * Field _showAllColLabels.
+     */
+    private boolean _showAllColLabels;
+
+    /**
+     * keeps track of state for field: _showAllColLabels
+     */
+    private boolean _has_showAllColLabels;
+
+    /**
+     * is an autocalculated annotation row
+     */
+    private boolean _autoCalculated = false;
+
+    /**
+     * keeps track of state for field: _autoCalculated
+     */
+    private boolean _has_autoCalculated;
+
+    /**
+     * Field _annotationElementList.
      */
     private java.util.Vector _annotationElementList;
 
     /**
-     * Field _label
+     * Field _label.
      */
     private java.lang.String _label;
 
     /**
-     * Field _description
+     * Field _description.
      */
     private java.lang.String _description;
 
     /**
-     * Field _thresholdLine
+     * Field _thresholdLine.
      */
     private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
 
@@ -132,8 +189,8 @@ public class Annotation implements java.io.Serializable {
 
     public Annotation() {
         super();
-        _annotationElementList = new Vector();
-    } //-- jalview.schemabinding.version2.Annotation()
+        this._annotationElementList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -141,582 +198,846 @@ public class Annotation implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addAnnotationElement
-     * 
      * 
      * 
      * @param vAnnotationElement
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.addElement(vAnnotationElement);
-    } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
+    public void addAnnotationElement(
+            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+    throws java.lang.IndexOutOfBoundsException {
+        this._annotationElementList.addElement(vAnnotationElement);
+    }
 
     /**
-     * Method addAnnotationElement
-     * 
      * 
      * 
      * @param index
      * @param vAnnotationElement
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.insertElementAt(vAnnotationElement, index);
-    } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
+    public void addAnnotationElement(
+            final int index,
+            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+    throws java.lang.IndexOutOfBoundsException {
+        this._annotationElementList.add(index, vAnnotationElement);
+    }
+
+    /**
+     */
+    public void deleteAutoCalculated(
+    ) {
+        this._has_autoCalculated= false;
+    }
+
+    /**
+     */
+    public void deleteCentreColLabels(
+    ) {
+        this._has_centreColLabels= false;
+    }
 
     /**
-     * Method deleteGraph
-     * 
      */
-    public void deleteGraph()
-    {
+    public void deleteGraph(
+    ) {
         this._has_graph= false;
-    } //-- void deleteGraph() 
+    }
 
     /**
-     * Method deleteGraphColour
-     * 
      */
-    public void deleteGraphColour()
-    {
+    public void deleteGraphColour(
+    ) {
         this._has_graphColour= false;
-    } //-- void deleteGraphColour() 
+    }
 
     /**
-     * Method deleteGraphGroup
-     * 
      */
-    public void deleteGraphGroup()
-    {
+    public void deleteGraphGroup(
+    ) {
         this._has_graphGroup= false;
-    } //-- void deleteGraphGroup() 
+    }
 
     /**
-     * Method deleteGraphType
-     * 
      */
-    public void deleteGraphType()
-    {
+    public void deleteGraphType(
+    ) {
         this._has_graphType= false;
-    } //-- void deleteGraphType() 
+    }
+
+    /**
+     */
+    public void deleteScaleColLabels(
+    ) {
+        this._has_scaleColLabels= false;
+    }
 
     /**
-     * Method deleteScore
-     * 
      */
-    public void deleteScore()
-    {
+    public void deleteScore(
+    ) {
         this._has_score= false;
-    } //-- void deleteScore() 
+    }
 
     /**
-     * Method deleteScoreOnly
-     * 
      */
-    public void deleteScoreOnly()
-    {
+    public void deleteScoreOnly(
+    ) {
         this._has_scoreOnly= false;
-    } //-- void deleteScoreOnly() 
+    }
 
     /**
-     * Method enumerateAnnotationElement
-     * 
-     * 
-     * 
-     * @return Enumeration
      */
-    public java.util.Enumeration enumerateAnnotationElement()
-    {
-        return _annotationElementList.elements();
-    } //-- java.util.Enumeration enumerateAnnotationElement() 
+    public void deleteShowAllColLabels(
+    ) {
+        this._has_showAllColLabels= false;
+    }
 
     /**
-     * Method getAnnotationElement
-     * 
+     */
+    public void deleteVisible(
+    ) {
+        this._has_visible= false;
+    }
+
+    /**
+     * Method enumerateAnnotationElement.
      * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.AnnotationElement elements
+     */
+    public java.util.Enumeration enumerateAnnotationElement(
+    ) {
+        return this._annotationElementList.elements();
+    }
+
+    /**
+     * Method getAnnotationElement.
      * 
      * @param index
-     * @return AnnotationElement
-     */
-    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.AnnotationElement at the
+     * given index
+     */
+    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._annotationElementList.size()) {
+            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
-    } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) 
+        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);
+    }
 
     /**
-     * Method getAnnotationElement
+     * Method getAnnotationElement.Returns the contents of the
+     * collection in an Array.  <p>Note:  Just in case the
+     * collection contents are changing in another thread, we pass
+     * a 0-length Array of the correct type into the API call. 
+     * This way we <i>know</i> that the Array returned is of
+     * exactly the correct length.
      * 
-     * 
-     * 
-     * @return AnnotationElement
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
-    {
-        int size = _annotationElementList.size();
-        jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() 
+    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(
+    ) {
+        jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+        return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
+    }
 
     /**
-     * Method getAnnotationElementCount
+     * Method getAnnotationElementCount.
      * 
+     * @return the size of this collection
+     */
+    public int getAnnotationElementCount(
+    ) {
+        return this._annotationElementList.size();
+    }
+
+    /**
+     * Returns the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
      * 
+     * @return the value of field 'AutoCalculated'.
+     */
+    public boolean getAutoCalculated(
+    ) {
+        return this._autoCalculated;
+    }
+
+    /**
+     * Returns the value of field 'centreColLabels'.
      * 
-     * @return int
+     * @return the value of field 'CentreColLabels'.
      */
-    public int getAnnotationElementCount()
-    {
-        return _annotationElementList.size();
-    } //-- int getAnnotationElementCount() 
+    public boolean getCentreColLabels(
+    ) {
+        return this._centreColLabels;
+    }
 
     /**
      * Returns the value of field 'description'.
      * 
-     * @return String
-     * @return the value of field 'description'.
+     * @return the value of field 'Description'.
      */
-    public java.lang.String getDescription()
-    {
+    public java.lang.String getDescription(
+    ) {
         return this._description;
-    } //-- java.lang.String getDescription() 
+    }
 
     /**
      * Returns the value of field 'graph'.
      * 
-     * @return boolean
-     * @return the value of field 'graph'.
+     * @return the value of field 'Graph'.
      */
-    public boolean getGraph()
-    {
+    public boolean getGraph(
+    ) {
         return this._graph;
-    } //-- boolean getGraph() 
+    }
 
     /**
      * Returns the value of field 'graphColour'.
      * 
-     * @return int
-     * @return the value of field 'graphColour'.
+     * @return the value of field 'GraphColour'.
      */
-    public int getGraphColour()
-    {
+    public int getGraphColour(
+    ) {
         return this._graphColour;
-    } //-- int getGraphColour() 
+    }
 
     /**
      * Returns the value of field 'graphGroup'.
      * 
-     * @return int
-     * @return the value of field 'graphGroup'.
+     * @return the value of field 'GraphGroup'.
      */
-    public int getGraphGroup()
-    {
+    public int getGraphGroup(
+    ) {
         return this._graphGroup;
-    } //-- int getGraphGroup() 
+    }
 
     /**
      * Returns the value of field 'graphType'.
      * 
-     * @return int
-     * @return the value of field 'graphType'.
+     * @return the value of field 'GraphType'.
      */
-    public int getGraphType()
-    {
+    public int getGraphType(
+    ) {
         return this._graphType;
-    } //-- int getGraphType() 
+    }
+
+    /**
+     * Returns the value of field 'groupRef'.
+     * 
+     * @return the value of field 'GroupRef'.
+     */
+    public java.lang.String getGroupRef(
+    ) {
+        return this._groupRef;
+    }
 
     /**
      * Returns the value of field 'id'.
      * 
-     * @return String
-     * @return the value of field 'id'.
+     * @return the value of field 'Id'.
      */
-    public java.lang.String getId()
-    {
+    public java.lang.String getId(
+    ) {
         return this._id;
-    } //-- java.lang.String getId() 
+    }
 
     /**
      * Returns the value of field 'label'.
      * 
-     * @return String
-     * @return the value of field 'label'.
+     * @return the value of field 'Label'.
      */
-    public java.lang.String getLabel()
-    {
+    public java.lang.String getLabel(
+    ) {
         return this._label;
-    } //-- java.lang.String getLabel() 
+    }
+
+    /**
+     * Returns the value of field 'scaleColLabels'.
+     * 
+     * @return the value of field 'ScaleColLabels'.
+     */
+    public boolean getScaleColLabels(
+    ) {
+        return this._scaleColLabels;
+    }
 
     /**
      * Returns the value of field 'score'.
      * 
-     * @return float
-     * @return the value of field 'score'.
+     * @return the value of field 'Score'.
      */
-    public float getScore()
-    {
+    public double getScore(
+    ) {
         return this._score;
-    } //-- float getScore() 
+    }
 
     /**
      * Returns the value of field 'scoreOnly'.
      * 
-     * @return boolean
-     * @return the value of field 'scoreOnly'.
+     * @return the value of field 'ScoreOnly'.
      */
-    public boolean getScoreOnly()
-    {
+    public boolean getScoreOnly(
+    ) {
         return this._scoreOnly;
-    } //-- boolean getScoreOnly() 
+    }
 
     /**
      * Returns the value of field 'sequenceRef'.
      * 
-     * @return String
-     * @return the value of field 'sequenceRef'.
+     * @return the value of field 'SequenceRef'.
      */
-    public java.lang.String getSequenceRef()
-    {
+    public java.lang.String getSequenceRef(
+    ) {
         return this._sequenceRef;
-    } //-- java.lang.String getSequenceRef() 
+    }
+
+    /**
+     * Returns the value of field 'showAllColLabels'.
+     * 
+     * @return the value of field 'ShowAllColLabels'.
+     */
+    public boolean getShowAllColLabels(
+    ) {
+        return this._showAllColLabels;
+    }
 
     /**
      * Returns the value of field 'thresholdLine'.
      * 
-     * @return ThresholdLine
-     * @return the value of field 'thresholdLine'.
+     * @return the value of field 'ThresholdLine'.
      */
-    public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
-    {
+    public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
+    ) {
         return this._thresholdLine;
-    } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() 
+    }
 
     /**
-     * Method hasGraph
-     * 
+     * Returns the value of field 'visible'.
      * 
+     * @return the value of field 'Visible'.
+     */
+    public boolean getVisible(
+    ) {
+        return this._visible;
+    }
+
+    /**
+     * Method hasAutoCalculated.
      * 
-     * @return boolean
+     * @return true if at least one AutoCalculated has been added
      */
-    public boolean hasGraph()
-    {
-        return this._has_graph;
-    } //-- boolean hasGraph() 
+    public boolean hasAutoCalculated(
+    ) {
+        return this._has_autoCalculated;
+    }
 
     /**
-     * Method hasGraphColour
+     * Method hasCentreColLabels.
      * 
+     * @return true if at least one CentreColLabels has been added
+     */
+    public boolean hasCentreColLabels(
+    ) {
+        return this._has_centreColLabels;
+    }
+
+    /**
+     * Method hasGraph.
      * 
+     * @return true if at least one Graph has been added
+     */
+    public boolean hasGraph(
+    ) {
+        return this._has_graph;
+    }
+
+    /**
+     * Method hasGraphColour.
      * 
-     * @return boolean
+     * @return true if at least one GraphColour has been added
      */
-    public boolean hasGraphColour()
-    {
+    public boolean hasGraphColour(
+    ) {
         return this._has_graphColour;
-    } //-- boolean hasGraphColour() 
+    }
 
     /**
-     * Method hasGraphGroup
-     * 
+     * Method hasGraphGroup.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one GraphGroup has been added
      */
-    public boolean hasGraphGroup()
-    {
+    public boolean hasGraphGroup(
+    ) {
         return this._has_graphGroup;
-    } //-- boolean hasGraphGroup() 
+    }
 
     /**
-     * Method hasGraphType
+     * Method hasGraphType.
      * 
+     * @return true if at least one GraphType has been added
+     */
+    public boolean hasGraphType(
+    ) {
+        return this._has_graphType;
+    }
+
+    /**
+     * Method hasScaleColLabels.
      * 
+     * @return true if at least one ScaleColLabels has been added
+     */
+    public boolean hasScaleColLabels(
+    ) {
+        return this._has_scaleColLabels;
+    }
+
+    /**
+     * Method hasScore.
      * 
-     * @return boolean
+     * @return true if at least one Score has been added
      */
-    public boolean hasGraphType()
-    {
-        return this._has_graphType;
-    } //-- boolean hasGraphType() 
+    public boolean hasScore(
+    ) {
+        return this._has_score;
+    }
 
     /**
-     * Method hasScore
+     * Method hasScoreOnly.
      * 
+     * @return true if at least one ScoreOnly has been added
+     */
+    public boolean hasScoreOnly(
+    ) {
+        return this._has_scoreOnly;
+    }
+
+    /**
+     * Method hasShowAllColLabels.
+     * 
+     * @return true if at least one ShowAllColLabels has been added
+     */
+    public boolean hasShowAllColLabels(
+    ) {
+        return this._has_showAllColLabels;
+    }
+
+    /**
+     * Method hasVisible.
      * 
+     * @return true if at least one Visible has been added
+     */
+    public boolean hasVisible(
+    ) {
+        return this._has_visible;
+    }
+
+    /**
+     * Returns the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
      * 
-     * @return boolean
+     * @return the value of field 'AutoCalculated'.
      */
-    public boolean hasScore()
-    {
-        return this._has_score;
-    } //-- boolean hasScore() 
+    public boolean isAutoCalculated(
+    ) {
+        return this._autoCalculated;
+    }
 
     /**
-     * Method hasScoreOnly
+     * Returns the value of field 'centreColLabels'.
      * 
+     * @return the value of field 'CentreColLabels'.
+     */
+    public boolean isCentreColLabels(
+    ) {
+        return this._centreColLabels;
+    }
+
+    /**
+     * Returns the value of field 'graph'.
      * 
+     * @return the value of field 'Graph'.
+     */
+    public boolean isGraph(
+    ) {
+        return this._graph;
+    }
+
+    /**
+     * Returns the value of field 'scaleColLabels'.
      * 
-     * @return boolean
+     * @return the value of field 'ScaleColLabels'.
      */
-    public boolean hasScoreOnly()
-    {
-        return this._has_scoreOnly;
-    } //-- boolean hasScoreOnly() 
+    public boolean isScaleColLabels(
+    ) {
+        return this._scaleColLabels;
+    }
 
     /**
-     * Method isValid
+     * Returns the value of field 'scoreOnly'.
      * 
+     * @return the value of field 'ScoreOnly'.
+     */
+    public boolean isScoreOnly(
+    ) {
+        return this._scoreOnly;
+    }
+
+    /**
+     * Returns the value of field 'showAllColLabels'.
      * 
+     * @return the value of field 'ShowAllColLabels'.
+     */
+    public boolean isShowAllColLabels(
+    ) {
+        return this._showAllColLabels;
+    }
+
+    /**
+     * Method isValid.
      * 
-     * @return boolean
+     * @return true if this object is valid according to the schema
      */
-    public boolean isValid()
-    {
+    public boolean isValid(
+    ) {
         try {
             validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        } catch (org.exolab.castor.xml.ValidationException vex) {
             return false;
         }
         return true;
-    } //-- boolean isValid() 
+    }
 
     /**
-     * Method marshal
+     * Returns the value of field 'visible'.
      * 
+     * @return the value of field 'Visible'.
+     */
+    public boolean isVisible(
+    ) {
+        return this._visible;
+    }
+
+    /**
      * 
      * 
      * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+     * @throws org.exolab.castor.xml.MarshalException 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);
-    } //-- void marshal(java.io.Writer) 
+    }
 
     /**
-     * Method marshal
-     * 
      * 
      * 
      * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+     * @throws java.io.IOException 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);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
 
     /**
-     * Method removeAllAnnotationElement
-     * 
      */
-    public void removeAllAnnotationElement()
-    {
-        _annotationElementList.removeAllElements();
-    } //-- void removeAllAnnotationElement() 
+    public void removeAllAnnotationElement(
+    ) {
+        this._annotationElementList.clear();
+    }
 
     /**
-     * Method removeAnnotationElement
-     * 
+     * Method removeAnnotationElement.
      * 
+     * @param vAnnotationElement
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeAnnotationElement(
+            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
+        boolean removed = _annotationElementList.remove(vAnnotationElement);
+        return removed;
+    }
+
+    /**
+     * Method removeAnnotationElementAt.
      * 
      * @param index
-     * @return AnnotationElement
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)
-    {
-        java.lang.Object obj = _annotationElementList.elementAt(index);
-        _annotationElementList.removeElementAt(index);
+    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+            final int index) {
+        java.lang.Object obj = this._annotationElementList.remove(index);
         return (jalview.schemabinding.version2.AnnotationElement) obj;
-    } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) 
+    }
 
     /**
-     * Method setAnnotationElement
-     * 
      * 
      * 
      * @param index
      * @param vAnnotationElement
-     */
-    public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setAnnotationElement(
+            final int index,
+            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._annotationElementList.size()) {
+            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
         }
-        _annotationElementList.setElementAt(vAnnotationElement, index);
-    } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
+        
+        this._annotationElementList.set(index, vAnnotationElement);
+    }
 
     /**
-     * Method setAnnotationElement
-     * 
      * 
      * 
-     * @param annotationElementArray
+     * @param vAnnotationElementArray
      */
-    public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)
-    {
+    public void setAnnotationElement(
+            final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {
         //-- copy array
-        _annotationElementList.removeAllElements();
-        for (int i = 0; i < annotationElementArray.length; i++) {
-            _annotationElementList.addElement(annotationElementArray[i]);
+        _annotationElementList.clear();
+        
+        for (int i = 0; i < vAnnotationElementArray.length; i++) {
+                this._annotationElementList.add(vAnnotationElementArray[i]);
         }
-    } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
+    }
+
+    /**
+     * Sets the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
+     * 
+     * @param autoCalculated the value of field 'autoCalculated'.
+     */
+    public void setAutoCalculated(
+            final boolean autoCalculated) {
+        this._autoCalculated = autoCalculated;
+        this._has_autoCalculated = true;
+    }
+
+    /**
+     * Sets the value of field 'centreColLabels'.
+     * 
+     * @param centreColLabels the value of field 'centreColLabels'.
+     */
+    public void setCentreColLabels(
+            final boolean centreColLabels) {
+        this._centreColLabels = centreColLabels;
+        this._has_centreColLabels = true;
+    }
 
     /**
      * Sets the value of field 'description'.
      * 
      * @param description the value of field 'description'.
      */
-    public void setDescription(java.lang.String description)
-    {
+    public void setDescription(
+            final java.lang.String description) {
         this._description = description;
-    } //-- void setDescription(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'graph'.
      * 
      * @param graph the value of field 'graph'.
      */
-    public void setGraph(boolean graph)
-    {
+    public void setGraph(
+            final boolean graph) {
         this._graph = graph;
         this._has_graph = true;
-    } //-- void setGraph(boolean) 
+    }
 
     /**
      * Sets the value of field 'graphColour'.
      * 
      * @param graphColour the value of field 'graphColour'.
      */
-    public void setGraphColour(int graphColour)
-    {
+    public void setGraphColour(
+            final int graphColour) {
         this._graphColour = graphColour;
         this._has_graphColour = true;
-    } //-- void setGraphColour(int) 
+    }
 
     /**
      * Sets the value of field 'graphGroup'.
      * 
      * @param graphGroup the value of field 'graphGroup'.
      */
-    public void setGraphGroup(int graphGroup)
-    {
+    public void setGraphGroup(
+            final int graphGroup) {
         this._graphGroup = graphGroup;
         this._has_graphGroup = true;
-    } //-- void setGraphGroup(int) 
+    }
 
     /**
      * Sets the value of field 'graphType'.
      * 
      * @param graphType the value of field 'graphType'.
      */
-    public void setGraphType(int graphType)
-    {
+    public void setGraphType(
+            final int graphType) {
         this._graphType = graphType;
         this._has_graphType = true;
-    } //-- void setGraphType(int) 
+    }
+
+    /**
+     * Sets the value of field 'groupRef'.
+     * 
+     * @param groupRef the value of field 'groupRef'.
+     */
+    public void setGroupRef(
+            final java.lang.String groupRef) {
+        this._groupRef = groupRef;
+    }
 
     /**
      * Sets the value of field 'id'.
      * 
      * @param id the value of field 'id'.
      */
-    public void setId(java.lang.String id)
-    {
+    public void setId(
+            final java.lang.String id) {
         this._id = id;
-    } //-- void setId(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'label'.
      * 
      * @param label the value of field 'label'.
      */
-    public void setLabel(java.lang.String label)
-    {
+    public void setLabel(
+            final java.lang.String label) {
         this._label = label;
-    } //-- void setLabel(java.lang.String) 
+    }
+
+    /**
+     * Sets the value of field 'scaleColLabels'.
+     * 
+     * @param scaleColLabels the value of field 'scaleColLabels'.
+     */
+    public void setScaleColLabels(
+            final boolean scaleColLabels) {
+        this._scaleColLabels = scaleColLabels;
+        this._has_scaleColLabels = true;
+    }
 
     /**
      * Sets the value of field 'score'.
      * 
      * @param score the value of field 'score'.
      */
-    public void setScore(float score)
-    {
+    public void setScore(
+            final double score) {
         this._score = score;
         this._has_score = true;
-    } //-- void setScore(float) 
+    }
 
     /**
      * Sets the value of field 'scoreOnly'.
      * 
      * @param scoreOnly the value of field 'scoreOnly'.
      */
-    public void setScoreOnly(boolean scoreOnly)
-    {
+    public void setScoreOnly(
+            final boolean scoreOnly) {
         this._scoreOnly = scoreOnly;
         this._has_scoreOnly = true;
-    } //-- void setScoreOnly(boolean) 
+    }
 
     /**
      * Sets the value of field 'sequenceRef'.
      * 
      * @param sequenceRef the value of field 'sequenceRef'.
      */
-    public void setSequenceRef(java.lang.String sequenceRef)
-    {
+    public void setSequenceRef(
+            final java.lang.String sequenceRef) {
         this._sequenceRef = sequenceRef;
-    } //-- void setSequenceRef(java.lang.String) 
+    }
+
+    /**
+     * Sets the value of field 'showAllColLabels'.
+     * 
+     * @param showAllColLabels the value of field 'showAllColLabels'
+     */
+    public void setShowAllColLabels(
+            final boolean showAllColLabels) {
+        this._showAllColLabels = showAllColLabels;
+        this._has_showAllColLabels = true;
+    }
 
     /**
      * Sets the value of field 'thresholdLine'.
      * 
      * @param thresholdLine the value of field 'thresholdLine'.
      */
-    public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)
-    {
+    public void setThresholdLine(
+            final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
         this._thresholdLine = thresholdLine;
-    } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) 
+    }
 
     /**
-     * Method unmarshal
-     * 
+     * Sets the value of field 'visible'.
      * 
+     * @param visible the value of field 'visible'.
+     */
+    public void setVisible(
+            final boolean visible) {
+        this._visible = visible;
+        this._has_visible = true;
+    }
+
+    /**
+     * Method unmarshal.
      * 
      * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
+     * @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.Annotation
+     */
+    public static jalview.schemabinding.version2.Annotation unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+    }
 
     /**
-     * Method validate
      * 
+     * 
+     * @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
-    {
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
 }