X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=06eb940abe27440ea2248f7b2814964b8ce6d099;hb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;hp=49edb8df01d66cbe9e42809152abb8adcdfb7fff;hpb=fae5909561b434d5fa0043584ace268c545dad9b;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 49edb8d..06eb940 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with
+ * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,906 +7,903 @@
 
 package jalview.schemabinding.version2;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
 
-import org.exolab.castor.xml.*;
+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 JGroup.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class JGroup
-    implements java.io.Serializable
-{
-
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
-
-  /**
-   * Field _start
-   */
-  private int _start;
-
-  /**
-   * keeps track of state for field: _start
-   */
-  private boolean _has_start;
-
-  /**
-   * Field _end
-   */
-  private int _end;
-
-  /**
-   * keeps track of state for field: _end
-   */
-  private boolean _has_end;
-
-  /**
-   * Field _name
-   */
-  private java.lang.String _name;
-
-  /**
-   * Field _colour
-   */
-  private java.lang.String _colour;
-
-  /**
-   * Field _consThreshold
-   */
-  private int _consThreshold;
-
-  /**
-   * keeps track of state for field: _consThreshold
-   */
-  private boolean _has_consThreshold;
-
-  /**
-   * Field _pidThreshold
-   */
-  private int _pidThreshold;
-
-  /**
-   * keeps track of state for field: _pidThreshold
-   */
-  private boolean _has_pidThreshold;
-
-  /**
-   * Field _outlineColour
-   */
-  private int _outlineColour;
-
-  /**
-   * keeps track of state for field: _outlineColour
-   */
-  private boolean _has_outlineColour;
-
-  /**
-   * Field _displayBoxes
-   */
-  private boolean _displayBoxes;
-
-  /**
-   * keeps track of state for field: _displayBoxes
-   */
-  private boolean _has_displayBoxes;
-
-  /**
-   * Field _displayText
-   */
-  private boolean _displayText;
-
-  /**
-   * keeps track of state for field: _displayText
-   */
-  private boolean _has_displayText;
-
-  /**
-   * Field _colourText
-   */
-  private boolean _colourText;
-
-  /**
-   * keeps track of state for field: _colourText
-   */
-  private boolean _has_colourText;
-
-  /**
-   * Field _textCol1
-   */
-  private int _textCol1;
-
-  /**
-   * keeps track of state for field: _textCol1
-   */
-  private boolean _has_textCol1;
-
-  /**
-   * Field _textCol2
-   */
-  private int _textCol2;
-
-  /**
-   * keeps track of state for field: _textCol2
-   */
-  private boolean _has_textCol2;
-
-  /**
-   * Field _textColThreshold
-   */
-  private int _textColThreshold;
-
-  /**
-   * keeps track of state for field: _textColThreshold
-   */
-  private boolean _has_textColThreshold;
-
-  /**
-   * Field _seqList
-   */
-  private java.util.Vector _seqList;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public JGroup()
-  {
-    super();
-    _seqList = new Vector();
-  } //-- jalview.schemabinding.version2.JGroup()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addSeq
-   *
-   *
-   *
-   * @param vSeq
-   */
-  public void addSeq(int vSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _seqList.addElement(new java.lang.Integer(vSeq));
-  } //-- void addSeq(int)
-
-  /**
-   * Method addSeq
-   *
-   *
-   *
-   * @param index
-   * @param vSeq
-   */
-  public void addSeq(int index, int vSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-  } //-- void addSeq(int, int)
-
-  /**
-   * Method deleteColourText
-   *
-   */
-  public void deleteColourText()
-  {
-    this._has_colourText = false;
-  } //-- void deleteColourText()
-
-  /**
-   * Method deleteConsThreshold
-   *
-   */
-  public void deleteConsThreshold()
-  {
-    this._has_consThreshold = false;
-  } //-- void deleteConsThreshold()
-
-  /**
-   * Method deleteDisplayBoxes
-   *
-   */
-  public void deleteDisplayBoxes()
-  {
-    this._has_displayBoxes = false;
-  } //-- void deleteDisplayBoxes()
-
-  /**
-   * Method deleteDisplayText
-   *
-   */
-  public void deleteDisplayText()
-  {
-    this._has_displayText = false;
-  } //-- void deleteDisplayText()
-
-  /**
-   * Method deleteEnd
-   *
-   */
-  public void deleteEnd()
-  {
-    this._has_end = false;
-  } //-- void deleteEnd()
-
-  /**
-   * Method deleteOutlineColour
-   *
-   */
-  public void deleteOutlineColour()
-  {
-    this._has_outlineColour = false;
-  } //-- void deleteOutlineColour()
-
-  /**
-   * Method deletePidThreshold
-   *
-   */
-  public void deletePidThreshold()
-  {
-    this._has_pidThreshold = false;
-  } //-- void deletePidThreshold()
-
-  /**
-   * Method deleteStart
-   *
-   */
-  public void deleteStart()
-  {
-    this._has_start = false;
-  } //-- void deleteStart()
-
-  /**
-   * Method deleteTextCol1
-   *
-   */
-  public void deleteTextCol1()
-  {
-    this._has_textCol1 = false;
-  } //-- void deleteTextCol1()
-
-  /**
-   * Method deleteTextCol2
-   *
-   */
-  public void deleteTextCol2()
-  {
-    this._has_textCol2 = false;
-  } //-- void deleteTextCol2()
-
-  /**
-   * Method deleteTextColThreshold
-   *
-   */
-  public void deleteTextColThreshold()
-  {
-    this._has_textColThreshold = false;
-  } //-- void deleteTextColThreshold()
-
-  /**
-   * Method enumerateSeq
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateSeq()
-  {
-    return _seqList.elements();
-  } //-- java.util.Enumeration enumerateSeq()
-
-  /**
-   * Returns the value of field 'colour'.
-   *
-   * @return String
-   * @return the value of field 'colour'.
-   */
-  public java.lang.String getColour()
-  {
-    return this._colour;
-  } //-- java.lang.String getColour()
-
-  /**
-   * Returns the value of field 'colourText'.
-   *
-   * @return boolean
-   * @return the value of field 'colourText'.
-   */
-  public boolean getColourText()
-  {
-    return this._colourText;
-  } //-- boolean getColourText()
-
-  /**
-   * Returns the value of field 'consThreshold'.
-   *
-   * @return int
-   * @return the value of field 'consThreshold'.
-   */
-  public int getConsThreshold()
-  {
-    return this._consThreshold;
-  } //-- int getConsThreshold()
-
-  /**
-   * Returns the value of field 'displayBoxes'.
-   *
-   * @return boolean
-   * @return the value of field 'displayBoxes'.
-   */
-  public boolean getDisplayBoxes()
-  {
-    return this._displayBoxes;
-  } //-- boolean getDisplayBoxes()
-
-  /**
-   * Returns the value of field 'displayText'.
-   *
-   * @return boolean
-   * @return the value of field 'displayText'.
-   */
-  public boolean getDisplayText()
-  {
-    return this._displayText;
-  } //-- boolean getDisplayText()
-
-  /**
-   * Returns the value of field 'end'.
-   *
-   * @return int
-   * @return the value of field 'end'.
-   */
-  public int getEnd()
-  {
-    return this._end;
-  } //-- int getEnd()
-
-  /**
-   * Returns the value of field 'name'.
-   *
-   * @return String
-   * @return the value of field 'name'.
-   */
-  public java.lang.String getName()
-  {
-    return this._name;
-  } //-- java.lang.String getName()
-
-  /**
-   * Returns the value of field 'outlineColour'.
-   *
-   * @return int
-   * @return the value of field 'outlineColour'.
-   */
-  public int getOutlineColour()
-  {
-    return this._outlineColour;
-  } //-- int getOutlineColour()
-
-  /**
-   * Returns the value of field 'pidThreshold'.
-   *
-   * @return int
-   * @return the value of field 'pidThreshold'.
-   */
-  public int getPidThreshold()
-  {
-    return this._pidThreshold;
-  } //-- int getPidThreshold()
-
-  /**
-   * Method getSeq
-   *
-   *
-   *
-   * @param index
-   * @return int
-   */
-  public int getSeq(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _seqList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return ( (java.lang.Integer) _seqList.elementAt(index)).intValue();
-  } //-- int getSeq(int)
-
-  /**
-   * Method getSeq
-   *
-   *
-   *
-   * @return int
-   */
-  public int[] getSeq()
-  {
-    int size = _seqList.size();
-    int[] mArray = new int[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = ( (java.lang.Integer) _seqList.elementAt(index)).intValue();
-    }
-    return mArray;
-  } //-- int[] getSeq()
-
-  /**
-   * Method getSeqCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getSeqCount()
-  {
-    return _seqList.size();
-  } //-- int getSeqCount()
-
-  /**
-   * Returns the value of field 'start'.
-   *
-   * @return int
-   * @return the value of field 'start'.
-   */
-  public int getStart()
-  {
-    return this._start;
-  } //-- int getStart()
-
-  /**
-   * Returns the value of field 'textCol1'.
-   *
-   * @return int
-   * @return the value of field 'textCol1'.
-   */
-  public int getTextCol1()
-  {
-    return this._textCol1;
-  } //-- int getTextCol1()
-
-  /**
-   * Returns the value of field 'textCol2'.
-   *
-   * @return int
-   * @return the value of field 'textCol2'.
-   */
-  public int getTextCol2()
-  {
-    return this._textCol2;
-  } //-- int getTextCol2()
-
-  /**
-   * Returns the value of field 'textColThreshold'.
-   *
-   * @return int
-   * @return the value of field 'textColThreshold'.
-   */
-  public int getTextColThreshold()
-  {
-    return this._textColThreshold;
-  } //-- int getTextColThreshold()
-
-  /**
-   * Method hasColourText
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasColourText()
-  {
-    return this._has_colourText;
-  } //-- boolean hasColourText()
-
-  /**
-   * Method hasConsThreshold
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasConsThreshold()
-  {
-    return this._has_consThreshold;
-  } //-- boolean hasConsThreshold()
-
-  /**
-   * Method hasDisplayBoxes
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasDisplayBoxes()
-  {
-    return this._has_displayBoxes;
-  } //-- boolean hasDisplayBoxes()
-
-  /**
-   * Method hasDisplayText
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasDisplayText()
-  {
-    return this._has_displayText;
-  } //-- boolean hasDisplayText()
-
-  /**
-   * Method hasEnd
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasEnd()
-  {
-    return this._has_end;
-  } //-- boolean hasEnd()
-
-  /**
-   * Method hasOutlineColour
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasOutlineColour()
-  {
-    return this._has_outlineColour;
-  } //-- boolean hasOutlineColour()
-
-  /**
-   * Method hasPidThreshold
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasPidThreshold()
-  {
-    return this._has_pidThreshold;
-  } //-- boolean hasPidThreshold()
-
-  /**
-   * Method hasStart
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasStart()
-  {
-    return this._has_start;
-  } //-- boolean hasStart()
-
-  /**
-   * Method hasTextCol1
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasTextCol1()
-  {
-    return this._has_textCol1;
-  } //-- boolean hasTextCol1()
-
-  /**
-   * Method hasTextCol2
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasTextCol2()
-  {
-    return this._has_textCol2;
-  } //-- boolean hasTextCol2()
-
-  /**
-   * Method hasTextColThreshold
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasTextColThreshold()
-  {
-    return this._has_textColThreshold;
-  } //-- boolean hasTextColThreshold()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    }
-    catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  } //-- boolean isValid()
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param out
-   */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param handler
-   */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, handler);
-  } //-- void marshal(org.xml.sax.ContentHandler)
-
-  /**
-   * Method removeAllSeq
-   *
-   */
-  public void removeAllSeq()
-  {
-    _seqList.removeAllElements();
-  } //-- void removeAllSeq()
-
-  /**
-   * Method removeSeq
-   *
-   *
-   *
-   * @param index
-   * @return int
-   */
-  public int removeSeq(int index)
-  {
-    java.lang.Object obj = _seqList.elementAt(index);
-    _seqList.removeElementAt(index);
-    return ( (java.lang.Integer) obj).intValue();
-  } //-- int removeSeq(int)
-
-  /**
-   * Sets the value of field 'colour'.
-   *
-   * @param colour the value of field 'colour'.
-   */
-  public void setColour(java.lang.String colour)
-  {
-    this._colour = colour;
-  } //-- void setColour(java.lang.String)
-
-  /**
-   * Sets the value of field 'colourText'.
-   *
-   * @param colourText the value of field 'colourText'.
-   */
-  public void setColourText(boolean colourText)
-  {
-    this._colourText = colourText;
-    this._has_colourText = true;
-  } //-- void setColourText(boolean)
-
-  /**
-   * Sets the value of field 'consThreshold'.
-   *
-   * @param consThreshold the value of field 'consThreshold'.
-   */
-  public void setConsThreshold(int consThreshold)
-  {
-    this._consThreshold = consThreshold;
-    this._has_consThreshold = true;
-  } //-- void setConsThreshold(int)
-
-  /**
-   * Sets the value of field 'displayBoxes'.
-   *
-   * @param displayBoxes the value of field 'displayBoxes'.
-   */
-  public void setDisplayBoxes(boolean displayBoxes)
-  {
-    this._displayBoxes = displayBoxes;
-    this._has_displayBoxes = true;
-  } //-- void setDisplayBoxes(boolean)
-
-  /**
-   * Sets the value of field 'displayText'.
-   *
-   * @param displayText the value of field 'displayText'.
-   */
-  public void setDisplayText(boolean displayText)
-  {
-    this._displayText = displayText;
-    this._has_displayText = true;
-  } //-- void setDisplayText(boolean)
-
-  /**
-   * Sets the value of field 'end'.
-   *
-   * @param end the value of field 'end'.
-   */
-  public void setEnd(int end)
-  {
-    this._end = end;
-    this._has_end = true;
-  } //-- void setEnd(int)
-
-  /**
-   * Sets the value of field 'name'.
-   *
-   * @param name the value of field 'name'.
-   */
-  public void setName(java.lang.String name)
-  {
-    this._name = name;
-  } //-- void setName(java.lang.String)
-
-  /**
-   * Sets the value of field 'outlineColour'.
-   *
-   * @param outlineColour the value of field 'outlineColour'.
-   */
-  public void setOutlineColour(int outlineColour)
-  {
-    this._outlineColour = outlineColour;
-    this._has_outlineColour = true;
-  } //-- void setOutlineColour(int)
-
-  /**
-   * Sets the value of field 'pidThreshold'.
-   *
-   * @param pidThreshold the value of field 'pidThreshold'.
-   */
-  public void setPidThreshold(int pidThreshold)
-  {
-    this._pidThreshold = pidThreshold;
-    this._has_pidThreshold = true;
-  } //-- void setPidThreshold(int)
-
-  /**
-   * Method setSeq
-   *
-   *
-   *
-   * @param index
-   * @param vSeq
-   */
-  public void setSeq(int index, int vSeq)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _seqList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _seqList.setElementAt(new java.lang.Integer(vSeq), index);
-  } //-- void setSeq(int, int)
-
-  /**
-   * Method setSeq
-   *
-   *
-   *
-   * @param seqArray
-   */
-  public void setSeq(int[] seqArray)
-  {
-    //-- copy array
-    _seqList.removeAllElements();
-    for (int i = 0; i < seqArray.length; i++)
-    {
-      _seqList.addElement(new java.lang.Integer(seqArray[i]));
-    }
-  } //-- void setSeq(int)
-
-  /**
-   * Sets the value of field 'start'.
-   *
-   * @param start the value of field 'start'.
-   */
-  public void setStart(int start)
-  {
-    this._start = start;
-    this._has_start = true;
-  } //-- void setStart(int)
-
-  /**
-   * Sets the value of field 'textCol1'.
-   *
-   * @param textCol1 the value of field 'textCol1'.
-   */
-  public void setTextCol1(int textCol1)
-  {
-    this._textCol1 = textCol1;
-    this._has_textCol1 = true;
-  } //-- void setTextCol1(int)
-
-  /**
-   * Sets the value of field 'textCol2'.
-   *
-   * @param textCol2 the value of field 'textCol2'.
-   */
-  public void setTextCol2(int textCol2)
-  {
-    this._textCol2 = textCol2;
-    this._has_textCol2 = true;
-  } //-- void setTextCol2(int)
-
-  /**
-   * Sets the value of field 'textColThreshold'.
-   *
-   * @param textColThreshold the value of field 'textColThreshold'
-   */
-  public void setTextColThreshold(int textColThreshold)
-  {
-    this._textColThreshold = textColThreshold;
-    this._has_textColThreshold = true;
-  } //-- void setTextColThreshold(int)
-
-  /**
-   * Method unmarshal
-   *
-   *
-   *
-   * @param reader
-   * @return Object
-   */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
-        jalview.schemabinding.version2.JGroup.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
-
-  /**
-   * Method validate
-   *
-   */
-  public void validate()
-      throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
-        Validator();
-    validator.validate(this);
-  } //-- void validate()
+public class JGroup implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _start
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _colour
+     */
+    private java.lang.String _colour;
+
+    /**
+     * Field _consThreshold
+     */
+    private int _consThreshold;
+
+    /**
+     * keeps track of state for field: _consThreshold
+     */
+    private boolean _has_consThreshold;
+
+    /**
+     * Field _pidThreshold
+     */
+    private int _pidThreshold;
+
+    /**
+     * keeps track of state for field: _pidThreshold
+     */
+    private boolean _has_pidThreshold;
+
+    /**
+     * Field _outlineColour
+     */
+    private int _outlineColour;
+
+    /**
+     * keeps track of state for field: _outlineColour
+     */
+    private boolean _has_outlineColour;
+
+    /**
+     * Field _displayBoxes
+     */
+    private boolean _displayBoxes;
+
+    /**
+     * keeps track of state for field: _displayBoxes
+     */
+    private boolean _has_displayBoxes;
+
+    /**
+     * Field _displayText
+     */
+    private boolean _displayText;
+
+    /**
+     * keeps track of state for field: _displayText
+     */
+    private boolean _has_displayText;
+
+    /**
+     * Field _colourText
+     */
+    private boolean _colourText;
+
+    /**
+     * keeps track of state for field: _colourText
+     */
+    private boolean _has_colourText;
+
+    /**
+     * Field _textCol1
+     */
+    private int _textCol1;
+
+    /**
+     * keeps track of state for field: _textCol1
+     */
+    private boolean _has_textCol1;
+
+    /**
+     * Field _textCol2
+     */
+    private int _textCol2;
+
+    /**
+     * keeps track of state for field: _textCol2
+     */
+    private boolean _has_textCol2;
+
+    /**
+     * Field _textColThreshold
+     */
+    private int _textColThreshold;
+
+    /**
+     * keeps track of state for field: _textColThreshold
+     */
+    private boolean _has_textColThreshold;
+
+    /**
+     * Field _seqList
+     */
+    private java.util.Vector _seqList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JGroup() {
+        super();
+        _seqList = new Vector();
+    } //-- jalview.schemabinding.version2.JGroup()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addSeq
+     * 
+     * 
+     * 
+     * @param vSeq
+     */
+    public void addSeq(int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _seqList.addElement(new java.lang.Integer(vSeq));
+    } //-- void addSeq(int) 
+
+    /**
+     * Method addSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     */
+    public void addSeq(int index, int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
+    } //-- void addSeq(int, int) 
+
+    /**
+     * Method deleteColourText
+     * 
+     */
+    public void deleteColourText()
+    {
+        this._has_colourText= false;
+    } //-- void deleteColourText() 
+
+    /**
+     * Method deleteConsThreshold
+     * 
+     */
+    public void deleteConsThreshold()
+    {
+        this._has_consThreshold= false;
+    } //-- void deleteConsThreshold() 
+
+    /**
+     * Method deleteDisplayBoxes
+     * 
+     */
+    public void deleteDisplayBoxes()
+    {
+        this._has_displayBoxes= false;
+    } //-- void deleteDisplayBoxes() 
+
+    /**
+     * Method deleteDisplayText
+     * 
+     */
+    public void deleteDisplayText()
+    {
+        this._has_displayText= false;
+    } //-- void deleteDisplayText() 
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
+     * Method deleteOutlineColour
+     * 
+     */
+    public void deleteOutlineColour()
+    {
+        this._has_outlineColour= false;
+    } //-- void deleteOutlineColour() 
+
+    /**
+     * Method deletePidThreshold
+     * 
+     */
+    public void deletePidThreshold()
+    {
+        this._has_pidThreshold= false;
+    } //-- void deletePidThreshold() 
+
+    /**
+     * Method deleteStart
+     * 
+     */
+    public void deleteStart()
+    {
+        this._has_start= false;
+    } //-- void deleteStart() 
+
+    /**
+     * Method deleteTextCol1
+     * 
+     */
+    public void deleteTextCol1()
+    {
+        this._has_textCol1= false;
+    } //-- void deleteTextCol1() 
+
+    /**
+     * Method deleteTextCol2
+     * 
+     */
+    public void deleteTextCol2()
+    {
+        this._has_textCol2= false;
+    } //-- void deleteTextCol2() 
+
+    /**
+     * Method deleteTextColThreshold
+     * 
+     */
+    public void deleteTextColThreshold()
+    {
+        this._has_textColThreshold= false;
+    } //-- void deleteTextColThreshold() 
+
+    /**
+     * Method enumerateSeq
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSeq()
+    {
+        return _seqList.elements();
+    } //-- java.util.Enumeration enumerateSeq() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return String
+     * @return the value of field 'colour'.
+     */
+    public java.lang.String getColour()
+    {
+        return this._colour;
+    } //-- java.lang.String getColour() 
+
+    /**
+     * Returns the value of field 'colourText'.
+     * 
+     * @return boolean
+     * @return the value of field 'colourText'.
+     */
+    public boolean getColourText()
+    {
+        return this._colourText;
+    } //-- boolean getColourText() 
+
+    /**
+     * Returns the value of field 'consThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'consThreshold'.
+     */
+    public int getConsThreshold()
+    {
+        return this._consThreshold;
+    } //-- int getConsThreshold() 
+
+    /**
+     * Returns the value of field 'displayBoxes'.
+     * 
+     * @return boolean
+     * @return the value of field 'displayBoxes'.
+     */
+    public boolean getDisplayBoxes()
+    {
+        return this._displayBoxes;
+    } //-- boolean getDisplayBoxes() 
+
+    /**
+     * Returns the value of field 'displayText'.
+     * 
+     * @return boolean
+     * @return the value of field 'displayText'.
+     */
+    public boolean getDisplayText()
+    {
+        return this._displayText;
+    } //-- boolean getDisplayText() 
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return int
+     * @return the value of field 'end'.
+     */
+    public int getEnd()
+    {
+        return this._end;
+    } //-- int getEnd() 
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'outlineColour'.
+     * 
+     * @return int
+     * @return the value of field 'outlineColour'.
+     */
+    public int getOutlineColour()
+    {
+        return this._outlineColour;
+    } //-- int getOutlineColour() 
+
+    /**
+     * Returns the value of field 'pidThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'pidThreshold'.
+     */
+    public int getPidThreshold()
+    {
+        return this._pidThreshold;
+    } //-- int getPidThreshold() 
+
+    /**
+     * Method getSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int getSeq(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _seqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+    } //-- int getSeq(int) 
+
+    /**
+     * Method getSeq
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int[] getSeq()
+    {
+        int size = _seqList.size();
+        int[] mArray = new int[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+        }
+        return mArray;
+    } //-- int[] getSeq() 
+
+    /**
+     * Method getSeqCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSeqCount()
+    {
+        return _seqList.size();
+    } //-- int getSeqCount() 
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return int
+     * @return the value of field 'start'.
+     */
+    public int getStart()
+    {
+        return this._start;
+    } //-- int getStart() 
+
+    /**
+     * Returns the value of field 'textCol1'.
+     * 
+     * @return int
+     * @return the value of field 'textCol1'.
+     */
+    public int getTextCol1()
+    {
+        return this._textCol1;
+    } //-- int getTextCol1() 
+
+    /**
+     * Returns the value of field 'textCol2'.
+     * 
+     * @return int
+     * @return the value of field 'textCol2'.
+     */
+    public int getTextCol2()
+    {
+        return this._textCol2;
+    } //-- int getTextCol2() 
+
+    /**
+     * Returns the value of field 'textColThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'textColThreshold'.
+     */
+    public int getTextColThreshold()
+    {
+        return this._textColThreshold;
+    } //-- int getTextColThreshold() 
+
+    /**
+     * Method hasColourText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColourText()
+    {
+        return this._has_colourText;
+    } //-- boolean hasColourText() 
+
+    /**
+     * Method hasConsThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConsThreshold()
+    {
+        return this._has_consThreshold;
+    } //-- boolean hasConsThreshold() 
+
+    /**
+     * Method hasDisplayBoxes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplayBoxes()
+    {
+        return this._has_displayBoxes;
+    } //-- boolean hasDisplayBoxes() 
+
+    /**
+     * Method hasDisplayText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplayText()
+    {
+        return this._has_displayText;
+    } //-- boolean hasDisplayText() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
+     * Method hasOutlineColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasOutlineColour()
+    {
+        return this._has_outlineColour;
+    } //-- boolean hasOutlineColour() 
+
+    /**
+     * Method hasPidThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidThreshold()
+    {
+        return this._has_pidThreshold;
+    } //-- boolean hasPidThreshold() 
+
+    /**
+     * Method hasStart
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStart()
+    {
+        return this._has_start;
+    } //-- boolean hasStart() 
+
+    /**
+     * Method hasTextCol1
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasTextCol1()
+    {
+        return this._has_textCol1;
+    } //-- boolean hasTextCol1() 
+
+    /**
+     * Method hasTextCol2
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasTextCol2()
+    {
+        return this._has_textCol2;
+    } //-- boolean hasTextCol2() 
+
+    /**
+     * Method hasTextColThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasTextColThreshold()
+    {
+        return this._has_textColThreshold;
+    } //-- boolean hasTextColThreshold() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllSeq
+     * 
+     */
+    public void removeAllSeq()
+    {
+        _seqList.removeAllElements();
+    } //-- void removeAllSeq() 
+
+    /**
+     * Method removeSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int removeSeq(int index)
+    {
+        java.lang.Object obj = _seqList.elementAt(index);
+        _seqList.removeElementAt(index);
+        return ((java.lang.Integer)obj).intValue();
+    } //-- int removeSeq(int) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(java.lang.String colour)
+    {
+        this._colour = colour;
+    } //-- void setColour(java.lang.String) 
+
+    /**
+     * Sets the value of field 'colourText'.
+     * 
+     * @param colourText the value of field 'colourText'.
+     */
+    public void setColourText(boolean colourText)
+    {
+        this._colourText = colourText;
+        this._has_colourText = true;
+    } //-- void setColourText(boolean) 
+
+    /**
+     * Sets the value of field 'consThreshold'.
+     * 
+     * @param consThreshold the value of field 'consThreshold'.
+     */
+    public void setConsThreshold(int consThreshold)
+    {
+        this._consThreshold = consThreshold;
+        this._has_consThreshold = true;
+    } //-- void setConsThreshold(int) 
+
+    /**
+     * Sets the value of field 'displayBoxes'.
+     * 
+     * @param displayBoxes the value of field 'displayBoxes'.
+     */
+    public void setDisplayBoxes(boolean displayBoxes)
+    {
+        this._displayBoxes = displayBoxes;
+        this._has_displayBoxes = true;
+    } //-- void setDisplayBoxes(boolean) 
+
+    /**
+     * Sets the value of field 'displayText'.
+     * 
+     * @param displayText the value of field 'displayText'.
+     */
+    public void setDisplayText(boolean displayText)
+    {
+        this._displayText = displayText;
+        this._has_displayText = true;
+    } //-- void setDisplayText(boolean) 
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(int end)
+    {
+        this._end = end;
+        this._has_end = true;
+    } //-- void setEnd(int) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'outlineColour'.
+     * 
+     * @param outlineColour the value of field 'outlineColour'.
+     */
+    public void setOutlineColour(int outlineColour)
+    {
+        this._outlineColour = outlineColour;
+        this._has_outlineColour = true;
+    } //-- void setOutlineColour(int) 
+
+    /**
+     * Sets the value of field 'pidThreshold'.
+     * 
+     * @param pidThreshold the value of field 'pidThreshold'.
+     */
+    public void setPidThreshold(int pidThreshold)
+    {
+        this._pidThreshold = pidThreshold;
+        this._has_pidThreshold = true;
+    } //-- void setPidThreshold(int) 
+
+    /**
+     * Method setSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     */
+    public void setSeq(int index, int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _seqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _seqList.setElementAt(new java.lang.Integer(vSeq), index);
+    } //-- void setSeq(int, int) 
+
+    /**
+     * Method setSeq
+     * 
+     * 
+     * 
+     * @param seqArray
+     */
+    public void setSeq(int[] seqArray)
+    {
+        //-- copy array
+        _seqList.removeAllElements();
+        for (int i = 0; i < seqArray.length; i++) {
+            _seqList.addElement(new java.lang.Integer(seqArray[i]));
+        }
+    } //-- void setSeq(int) 
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(int start)
+    {
+        this._start = start;
+        this._has_start = true;
+    } //-- void setStart(int) 
+
+    /**
+     * Sets the value of field 'textCol1'.
+     * 
+     * @param textCol1 the value of field 'textCol1'.
+     */
+    public void setTextCol1(int textCol1)
+    {
+        this._textCol1 = textCol1;
+        this._has_textCol1 = true;
+    } //-- void setTextCol1(int) 
+
+    /**
+     * Sets the value of field 'textCol2'.
+     * 
+     * @param textCol2 the value of field 'textCol2'.
+     */
+    public void setTextCol2(int textCol2)
+    {
+        this._textCol2 = textCol2;
+        this._has_textCol2 = true;
+    } //-- void setTextCol2(int) 
+
+    /**
+     * Sets the value of field 'textColThreshold'.
+     * 
+     * @param textColThreshold the value of field 'textColThreshold'
+     */
+    public void setTextColThreshold(int textColThreshold)
+    {
+        this._textColThreshold = textColThreshold;
+        this._has_textColThreshold = true;
+    } //-- void setTextColThreshold(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
 
 }