X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FViewport.java;h=911061b3e38bcddd0d54dfb57d8bd9501f458fee;hb=a87f4c6fd568ccf29aaf3af0ad528da442ea921d;hp=07622b36a63923c809dfb08ad4e34c740121598c;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index 07622b3..911061b 100755
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.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.
  * $Id$
@@ -7,1413 +7,1414 @@
 
 package jalview.binding;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.xml.*;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
 
 /**
  * Class Viewport.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class Viewport
-    implements java.io.Serializable
-{
-
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
-
-  /**
-   * Field _conservationSelected
-   */
-  private boolean _conservationSelected;
-
-  /**
-   * keeps track of state for field: _conservationSelected
-   */
-  private boolean _has_conservationSelected;
-
-  /**
-   * Field _pidSelected
-   */
-  private boolean _pidSelected;
-
-  /**
-   * keeps track of state for field: _pidSelected
-   */
-  private boolean _has_pidSelected;
-
-  /**
-   * Field _bgColour
-   */
-  private java.lang.String _bgColour;
-
-  /**
-   * 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 _title
-   */
-  private java.lang.String _title;
-
-  /**
-   * Field _showFullId
-   */
-  private boolean _showFullId;
-
-  /**
-   * keeps track of state for field: _showFullId
-   */
-  private boolean _has_showFullId;
-
-  /**
-   * Field _showText
-   */
-  private boolean _showText;
-
-  /**
-   * keeps track of state for field: _showText
-   */
-  private boolean _has_showText;
-
-  /**
-   * Field _showColourText
-   */
-  private boolean _showColourText;
-
-  /**
-   * keeps track of state for field: _showColourText
-   */
-  private boolean _has_showColourText;
-
-  /**
-   * Field _showBoxes
-   */
-  private boolean _showBoxes;
-
-  /**
-   * keeps track of state for field: _showBoxes
-   */
-  private boolean _has_showBoxes;
-
-  /**
-   * Field _wrapAlignment
-   */
-  private boolean _wrapAlignment;
-
-  /**
-   * keeps track of state for field: _wrapAlignment
-   */
-  private boolean _has_wrapAlignment;
-
-  /**
-   * Field _renderGaps
-   */
-  private boolean _renderGaps;
-
-  /**
-   * keeps track of state for field: _renderGaps
-   */
-  private boolean _has_renderGaps;
-
-  /**
-   * Field _showSequenceFeatures
-   */
-  private boolean _showSequenceFeatures;
-
-  /**
-   * keeps track of state for field: _showSequenceFeatures
-   */
-  private boolean _has_showSequenceFeatures;
-
-  /**
-   * Field _showAnnotation
-   */
-  private boolean _showAnnotation;
-
-  /**
-   * keeps track of state for field: _showAnnotation
-   */
-  private boolean _has_showAnnotation;
-
-  /**
-   * Field _showConservation
-   */
-  private boolean _showConservation;
-
-  /**
-   * keeps track of state for field: _showConservation
-   */
-  private boolean _has_showConservation;
-
-  /**
-   * Field _showQuality
-   */
-  private boolean _showQuality;
-
-  /**
-   * keeps track of state for field: _showQuality
-   */
-  private boolean _has_showQuality;
-
-  /**
-   * Field _showIdentity
-   */
-  private boolean _showIdentity;
-
-  /**
-   * keeps track of state for field: _showIdentity
-   */
-  private boolean _has_showIdentity;
-
-  /**
-   * Field _xpos
-   */
-  private int _xpos;
-
-  /**
-   * keeps track of state for field: _xpos
-   */
-  private boolean _has_xpos;
-
-  /**
-   * Field _ypos
-   */
-  private int _ypos;
-
-  /**
-   * keeps track of state for field: _ypos
-   */
-  private boolean _has_ypos;
-
-  /**
-   * Field _width
-   */
-  private int _width;
-
-  /**
-   * keeps track of state for field: _width
-   */
-  private boolean _has_width;
-
-  /**
-   * Field _height
-   */
-  private int _height;
-
-  /**
-   * keeps track of state for field: _height
-   */
-  private boolean _has_height;
-
-  /**
-   * Field _startRes
-   */
-  private int _startRes;
-
-  /**
-   * keeps track of state for field: _startRes
-   */
-  private boolean _has_startRes;
-
-  /**
-   * Field _startSeq
-   */
-  private int _startSeq;
-
-  /**
-   * keeps track of state for field: _startSeq
-   */
-  private boolean _has_startSeq;
-
-  /**
-   * Field _fontName
-   */
-  private java.lang.String _fontName;
-
-  /**
-   * Field _fontSize
-   */
-  private int _fontSize;
-
-  /**
-   * keeps track of state for field: _fontSize
-   */
-  private boolean _has_fontSize;
-
-  /**
-   * Field _fontStyle
-   */
-  private int _fontStyle;
-
-  /**
-   * keeps track of state for field: _fontStyle
-   */
-  private boolean _has_fontStyle;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public Viewport()
-  {
-    super();
-  } //-- jalview.binding.Viewport()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method deleteConsThreshold
-   *
-   */
-  public void deleteConsThreshold()
-  {
-    this._has_consThreshold = false;
-  } //-- void deleteConsThreshold()
-
-  /**
-   * Method deleteConservationSelected
-   *
-   */
-  public void deleteConservationSelected()
-  {
-    this._has_conservationSelected = false;
-  } //-- void deleteConservationSelected()
-
-  /**
-   * Method deleteFontSize
-   *
-   */
-  public void deleteFontSize()
-  {
-    this._has_fontSize = false;
-  } //-- void deleteFontSize()
-
-  /**
-   * Method deleteFontStyle
-   *
-   */
-  public void deleteFontStyle()
-  {
-    this._has_fontStyle = false;
-  } //-- void deleteFontStyle()
-
-  /**
-   * Method deleteHeight
-   *
-   */
-  public void deleteHeight()
-  {
-    this._has_height = false;
-  } //-- void deleteHeight()
-
-  /**
-   * Method deletePidSelected
-   *
-   */
-  public void deletePidSelected()
-  {
-    this._has_pidSelected = false;
-  } //-- void deletePidSelected()
-
-  /**
-   * Method deletePidThreshold
-   *
-   */
-  public void deletePidThreshold()
-  {
-    this._has_pidThreshold = false;
-  } //-- void deletePidThreshold()
-
-  /**
-   * Method deleteRenderGaps
-   *
-   */
-  public void deleteRenderGaps()
-  {
-    this._has_renderGaps = false;
-  } //-- void deleteRenderGaps()
-
-  /**
-   * Method deleteShowAnnotation
-   *
-   */
-  public void deleteShowAnnotation()
-  {
-    this._has_showAnnotation = false;
-  } //-- void deleteShowAnnotation()
-
-  /**
-   * Method deleteShowBoxes
-   *
-   */
-  public void deleteShowBoxes()
-  {
-    this._has_showBoxes = false;
-  } //-- void deleteShowBoxes()
-
-  /**
-   * Method deleteShowColourText
-   *
-   */
-  public void deleteShowColourText()
-  {
-    this._has_showColourText = false;
-  } //-- void deleteShowColourText()
-
-  /**
-   * Method deleteShowConservation
-   *
-   */
-  public void deleteShowConservation()
-  {
-    this._has_showConservation = false;
-  } //-- void deleteShowConservation()
-
-  /**
-   * Method deleteShowFullId
-   *
-   */
-  public void deleteShowFullId()
-  {
-    this._has_showFullId = false;
-  } //-- void deleteShowFullId()
-
-  /**
-   * Method deleteShowIdentity
-   *
-   */
-  public void deleteShowIdentity()
-  {
-    this._has_showIdentity = false;
-  } //-- void deleteShowIdentity()
-
-  /**
-   * Method deleteShowQuality
-   *
-   */
-  public void deleteShowQuality()
-  {
-    this._has_showQuality = false;
-  } //-- void deleteShowQuality()
-
-  /**
-   * Method deleteShowSequenceFeatures
-   *
-   */
-  public void deleteShowSequenceFeatures()
-  {
-    this._has_showSequenceFeatures = false;
-  } //-- void deleteShowSequenceFeatures()
-
-  /**
-   * Method deleteShowText
-   *
-   */
-  public void deleteShowText()
-  {
-    this._has_showText = false;
-  } //-- void deleteShowText()
-
-  /**
-   * Method deleteStartRes
-   *
-   */
-  public void deleteStartRes()
-  {
-    this._has_startRes = false;
-  } //-- void deleteStartRes()
-
-  /**
-   * Method deleteStartSeq
-   *
-   */
-  public void deleteStartSeq()
-  {
-    this._has_startSeq = false;
-  } //-- void deleteStartSeq()
-
-  /**
-   * Method deleteWidth
-   *
-   */
-  public void deleteWidth()
-  {
-    this._has_width = false;
-  } //-- void deleteWidth()
-
-  /**
-   * Method deleteWrapAlignment
-   *
-   */
-  public void deleteWrapAlignment()
-  {
-    this._has_wrapAlignment = false;
-  } //-- void deleteWrapAlignment()
-
-  /**
-   * Method deleteXpos
-   *
-   */
-  public void deleteXpos()
-  {
-    this._has_xpos = false;
-  } //-- void deleteXpos()
-
-  /**
-   * Method deleteYpos
-   *
-   */
-  public void deleteYpos()
-  {
-    this._has_ypos = false;
-  } //-- void deleteYpos()
-
-  /**
-   * Returns the value of field 'bgColour'.
-   *
-   * @return String
-   * @return the value of field 'bgColour'.
-   */
-  public java.lang.String getBgColour()
-  {
-    return this._bgColour;
-  } //-- java.lang.String getBgColour()
-
-  /**
-   * 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 'conservationSelected'.
-   *
-   * @return boolean
-   * @return the value of field 'conservationSelected'.
-   */
-  public boolean getConservationSelected()
-  {
-    return this._conservationSelected;
-  } //-- boolean getConservationSelected()
-
-  /**
-   * Returns the value of field 'fontName'.
-   *
-   * @return String
-   * @return the value of field 'fontName'.
-   */
-  public java.lang.String getFontName()
-  {
-    return this._fontName;
-  } //-- java.lang.String getFontName()
-
-  /**
-   * Returns the value of field 'fontSize'.
-   *
-   * @return int
-   * @return the value of field 'fontSize'.
-   */
-  public int getFontSize()
-  {
-    return this._fontSize;
-  } //-- int getFontSize()
-
-  /**
-   * Returns the value of field 'fontStyle'.
-   *
-   * @return int
-   * @return the value of field 'fontStyle'.
-   */
-  public int getFontStyle()
-  {
-    return this._fontStyle;
-  } //-- int getFontStyle()
-
-  /**
-   * Returns the value of field 'height'.
-   *
-   * @return int
-   * @return the value of field 'height'.
-   */
-  public int getHeight()
-  {
-    return this._height;
-  } //-- int getHeight()
-
-  /**
-   * Returns the value of field 'pidSelected'.
-   *
-   * @return boolean
-   * @return the value of field 'pidSelected'.
-   */
-  public boolean getPidSelected()
-  {
-    return this._pidSelected;
-  } //-- boolean getPidSelected()
-
-  /**
-   * Returns the value of field 'pidThreshold'.
-   *
-   * @return int
-   * @return the value of field 'pidThreshold'.
-   */
-  public int getPidThreshold()
-  {
-    return this._pidThreshold;
-  } //-- int getPidThreshold()
-
-  /**
-   * Returns the value of field 'renderGaps'.
-   *
-   * @return boolean
-   * @return the value of field 'renderGaps'.
-   */
-  public boolean getRenderGaps()
-  {
-    return this._renderGaps;
-  } //-- boolean getRenderGaps()
-
-  /**
-   * Returns the value of field 'showAnnotation'.
-   *
-   * @return boolean
-   * @return the value of field 'showAnnotation'.
-   */
-  public boolean getShowAnnotation()
-  {
-    return this._showAnnotation;
-  } //-- boolean getShowAnnotation()
-
-  /**
-   * Returns the value of field 'showBoxes'.
-   *
-   * @return boolean
-   * @return the value of field 'showBoxes'.
-   */
-  public boolean getShowBoxes()
-  {
-    return this._showBoxes;
-  } //-- boolean getShowBoxes()
-
-  /**
-   * Returns the value of field 'showColourText'.
-   *
-   * @return boolean
-   * @return the value of field 'showColourText'.
-   */
-  public boolean getShowColourText()
-  {
-    return this._showColourText;
-  } //-- boolean getShowColourText()
-
-  /**
-   * Returns the value of field 'showConservation'.
-   *
-   * @return boolean
-   * @return the value of field 'showConservation'.
-   */
-  public boolean getShowConservation()
-  {
-    return this._showConservation;
-  } //-- boolean getShowConservation()
-
-  /**
-   * Returns the value of field 'showFullId'.
-   *
-   * @return boolean
-   * @return the value of field 'showFullId'.
-   */
-  public boolean getShowFullId()
-  {
-    return this._showFullId;
-  } //-- boolean getShowFullId()
-
-  /**
-   * Returns the value of field 'showIdentity'.
-   *
-   * @return boolean
-   * @return the value of field 'showIdentity'.
-   */
-  public boolean getShowIdentity()
-  {
-    return this._showIdentity;
-  } //-- boolean getShowIdentity()
-
-  /**
-   * Returns the value of field 'showQuality'.
-   *
-   * @return boolean
-   * @return the value of field 'showQuality'.
-   */
-  public boolean getShowQuality()
-  {
-    return this._showQuality;
-  } //-- boolean getShowQuality()
-
-  /**
-   * Returns the value of field 'showSequenceFeatures'.
-   *
-   * @return boolean
-   * @return the value of field 'showSequenceFeatures'.
-   */
-  public boolean getShowSequenceFeatures()
-  {
-    return this._showSequenceFeatures;
-  } //-- boolean getShowSequenceFeatures()
-
-  /**
-   * Returns the value of field 'showText'.
-   *
-   * @return boolean
-   * @return the value of field 'showText'.
-   */
-  public boolean getShowText()
-  {
-    return this._showText;
-  } //-- boolean getShowText()
-
-  /**
-   * Returns the value of field 'startRes'.
-   *
-   * @return int
-   * @return the value of field 'startRes'.
-   */
-  public int getStartRes()
-  {
-    return this._startRes;
-  } //-- int getStartRes()
-
-  /**
-   * Returns the value of field 'startSeq'.
-   *
-   * @return int
-   * @return the value of field 'startSeq'.
-   */
-  public int getStartSeq()
-  {
-    return this._startSeq;
-  } //-- int getStartSeq()
-
-  /**
-   * Returns the value of field 'title'.
-   *
-   * @return String
-   * @return the value of field 'title'.
-   */
-  public java.lang.String getTitle()
-  {
-    return this._title;
-  } //-- java.lang.String getTitle()
-
-  /**
-   * Returns the value of field 'width'.
-   *
-   * @return int
-   * @return the value of field 'width'.
-   */
-  public int getWidth()
-  {
-    return this._width;
-  } //-- int getWidth()
-
-  /**
-   * Returns the value of field 'wrapAlignment'.
-   *
-   * @return boolean
-   * @return the value of field 'wrapAlignment'.
-   */
-  public boolean getWrapAlignment()
-  {
-    return this._wrapAlignment;
-  } //-- boolean getWrapAlignment()
-
-  /**
-   * Returns the value of field 'xpos'.
-   *
-   * @return int
-   * @return the value of field 'xpos'.
-   */
-  public int getXpos()
-  {
-    return this._xpos;
-  } //-- int getXpos()
-
-  /**
-   * Returns the value of field 'ypos'.
-   *
-   * @return int
-   * @return the value of field 'ypos'.
-   */
-  public int getYpos()
-  {
-    return this._ypos;
-  } //-- int getYpos()
-
-  /**
-   * Method hasConsThreshold
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasConsThreshold()
-  {
-    return this._has_consThreshold;
-  } //-- boolean hasConsThreshold()
-
-  /**
-   * Method hasConservationSelected
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasConservationSelected()
-  {
-    return this._has_conservationSelected;
-  } //-- boolean hasConservationSelected()
-
-  /**
-   * Method hasFontSize
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasFontSize()
-  {
-    return this._has_fontSize;
-  } //-- boolean hasFontSize()
-
-  /**
-   * Method hasFontStyle
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasFontStyle()
-  {
-    return this._has_fontStyle;
-  } //-- boolean hasFontStyle()
-
-  /**
-   * Method hasHeight
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasHeight()
-  {
-    return this._has_height;
-  } //-- boolean hasHeight()
-
-  /**
-   * Method hasPidSelected
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasPidSelected()
-  {
-    return this._has_pidSelected;
-  } //-- boolean hasPidSelected()
-
-  /**
-   * Method hasPidThreshold
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasPidThreshold()
-  {
-    return this._has_pidThreshold;
-  } //-- boolean hasPidThreshold()
-
-  /**
-   * Method hasRenderGaps
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasRenderGaps()
-  {
-    return this._has_renderGaps;
-  } //-- boolean hasRenderGaps()
-
-  /**
-   * Method hasShowAnnotation
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowAnnotation()
-  {
-    return this._has_showAnnotation;
-  } //-- boolean hasShowAnnotation()
-
-  /**
-   * Method hasShowBoxes
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowBoxes()
-  {
-    return this._has_showBoxes;
-  } //-- boolean hasShowBoxes()
-
-  /**
-   * Method hasShowColourText
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowColourText()
-  {
-    return this._has_showColourText;
-  } //-- boolean hasShowColourText()
-
-  /**
-   * Method hasShowConservation
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowConservation()
-  {
-    return this._has_showConservation;
-  } //-- boolean hasShowConservation()
-
-  /**
-   * Method hasShowFullId
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowFullId()
-  {
-    return this._has_showFullId;
-  } //-- boolean hasShowFullId()
-
-  /**
-   * Method hasShowIdentity
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowIdentity()
-  {
-    return this._has_showIdentity;
-  } //-- boolean hasShowIdentity()
-
-  /**
-   * Method hasShowQuality
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowQuality()
-  {
-    return this._has_showQuality;
-  } //-- boolean hasShowQuality()
-
-  /**
-   * Method hasShowSequenceFeatures
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowSequenceFeatures()
-  {
-    return this._has_showSequenceFeatures;
-  } //-- boolean hasShowSequenceFeatures()
-
-  /**
-   * Method hasShowText
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasShowText()
-  {
-    return this._has_showText;
-  } //-- boolean hasShowText()
-
-  /**
-   * Method hasStartRes
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasStartRes()
-  {
-    return this._has_startRes;
-  } //-- boolean hasStartRes()
-
-  /**
-   * Method hasStartSeq
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasStartSeq()
-  {
-    return this._has_startSeq;
-  } //-- boolean hasStartSeq()
-
-  /**
-   * Method hasWidth
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasWidth()
-  {
-    return this._has_width;
-  } //-- boolean hasWidth()
-
-  /**
-   * Method hasWrapAlignment
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasWrapAlignment()
-  {
-    return this._has_wrapAlignment;
-  } //-- boolean hasWrapAlignment()
-
-  /**
-   * Method hasXpos
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasXpos()
-  {
-    return this._has_xpos;
-  } //-- boolean hasXpos()
-
-  /**
-   * Method hasYpos
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasYpos()
-  {
-    return this._has_ypos;
-  } //-- boolean hasYpos()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    }
-    catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  } //-- boolean isValid()
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param out
-   */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param handler
-   */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, handler);
-  } //-- void marshal(org.xml.sax.ContentHandler)
-
-  /**
-   * Sets the value of field 'bgColour'.
-   *
-   * @param bgColour the value of field 'bgColour'.
-   */
-  public void setBgColour(java.lang.String bgColour)
-  {
-    this._bgColour = bgColour;
-  } //-- void setBgColour(java.lang.String)
-
-  /**
-   * 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 'conservationSelected'.
-   *
-   * @param conservationSelected the value of field
-   * 'conservationSelected'.
-   */
-  public void setConservationSelected(boolean conservationSelected)
-  {
-    this._conservationSelected = conservationSelected;
-    this._has_conservationSelected = true;
-  } //-- void setConservationSelected(boolean)
-
-  /**
-   * Sets the value of field 'fontName'.
-   *
-   * @param fontName the value of field 'fontName'.
-   */
-  public void setFontName(java.lang.String fontName)
-  {
-    this._fontName = fontName;
-  } //-- void setFontName(java.lang.String)
-
-  /**
-   * Sets the value of field 'fontSize'.
-   *
-   * @param fontSize the value of field 'fontSize'.
-   */
-  public void setFontSize(int fontSize)
-  {
-    this._fontSize = fontSize;
-    this._has_fontSize = true;
-  } //-- void setFontSize(int)
-
-  /**
-   * Sets the value of field 'fontStyle'.
-   *
-   * @param fontStyle the value of field 'fontStyle'.
-   */
-  public void setFontStyle(int fontStyle)
-  {
-    this._fontStyle = fontStyle;
-    this._has_fontStyle = true;
-  } //-- void setFontStyle(int)
-
-  /**
-   * Sets the value of field 'height'.
-   *
-   * @param height the value of field 'height'.
-   */
-  public void setHeight(int height)
-  {
-    this._height = height;
-    this._has_height = true;
-  } //-- void setHeight(int)
-
-  /**
-   * Sets the value of field 'pidSelected'.
-   *
-   * @param pidSelected the value of field 'pidSelected'.
-   */
-  public void setPidSelected(boolean pidSelected)
-  {
-    this._pidSelected = pidSelected;
-    this._has_pidSelected = true;
-  } //-- void setPidSelected(boolean)
-
-  /**
-   * 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)
-
-  /**
-   * Sets the value of field 'renderGaps'.
-   *
-   * @param renderGaps the value of field 'renderGaps'.
-   */
-  public void setRenderGaps(boolean renderGaps)
-  {
-    this._renderGaps = renderGaps;
-    this._has_renderGaps = true;
-  } //-- void setRenderGaps(boolean)
-
-  /**
-   * Sets the value of field 'showAnnotation'.
-   *
-   * @param showAnnotation the value of field 'showAnnotation'.
-   */
-  public void setShowAnnotation(boolean showAnnotation)
-  {
-    this._showAnnotation = showAnnotation;
-    this._has_showAnnotation = true;
-  } //-- void setShowAnnotation(boolean)
-
-  /**
-   * Sets the value of field 'showBoxes'.
-   *
-   * @param showBoxes the value of field 'showBoxes'.
-   */
-  public void setShowBoxes(boolean showBoxes)
-  {
-    this._showBoxes = showBoxes;
-    this._has_showBoxes = true;
-  } //-- void setShowBoxes(boolean)
-
-  /**
-   * Sets the value of field 'showColourText'.
-   *
-   * @param showColourText the value of field 'showColourText'.
-   */
-  public void setShowColourText(boolean showColourText)
-  {
-    this._showColourText = showColourText;
-    this._has_showColourText = true;
-  } //-- void setShowColourText(boolean)
-
-  /**
-   * Sets the value of field 'showConservation'.
-   *
-   * @param showConservation the value of field 'showConservation'
-   */
-  public void setShowConservation(boolean showConservation)
-  {
-    this._showConservation = showConservation;
-    this._has_showConservation = true;
-  } //-- void setShowConservation(boolean)
-
-  /**
-   * Sets the value of field 'showFullId'.
-   *
-   * @param showFullId the value of field 'showFullId'.
-   */
-  public void setShowFullId(boolean showFullId)
-  {
-    this._showFullId = showFullId;
-    this._has_showFullId = true;
-  } //-- void setShowFullId(boolean)
-
-  /**
-   * Sets the value of field 'showIdentity'.
-   *
-   * @param showIdentity the value of field 'showIdentity'.
-   */
-  public void setShowIdentity(boolean showIdentity)
-  {
-    this._showIdentity = showIdentity;
-    this._has_showIdentity = true;
-  } //-- void setShowIdentity(boolean)
-
-  /**
-   * Sets the value of field 'showQuality'.
-   *
-   * @param showQuality the value of field 'showQuality'.
-   */
-  public void setShowQuality(boolean showQuality)
-  {
-    this._showQuality = showQuality;
-    this._has_showQuality = true;
-  } //-- void setShowQuality(boolean)
-
-  /**
-   * Sets the value of field 'showSequenceFeatures'.
-   *
-   * @param showSequenceFeatures the value of field
-   * 'showSequenceFeatures'.
-   */
-  public void setShowSequenceFeatures(boolean showSequenceFeatures)
-  {
-    this._showSequenceFeatures = showSequenceFeatures;
-    this._has_showSequenceFeatures = true;
-  } //-- void setShowSequenceFeatures(boolean)
-
-  /**
-   * Sets the value of field 'showText'.
-   *
-   * @param showText the value of field 'showText'.
-   */
-  public void setShowText(boolean showText)
-  {
-    this._showText = showText;
-    this._has_showText = true;
-  } //-- void setShowText(boolean)
-
-  /**
-   * Sets the value of field 'startRes'.
-   *
-   * @param startRes the value of field 'startRes'.
-   */
-  public void setStartRes(int startRes)
-  {
-    this._startRes = startRes;
-    this._has_startRes = true;
-  } //-- void setStartRes(int)
-
-  /**
-   * Sets the value of field 'startSeq'.
-   *
-   * @param startSeq the value of field 'startSeq'.
-   */
-  public void setStartSeq(int startSeq)
-  {
-    this._startSeq = startSeq;
-    this._has_startSeq = true;
-  } //-- void setStartSeq(int)
-
-  /**
-   * Sets the value of field 'title'.
-   *
-   * @param title the value of field 'title'.
-   */
-  public void setTitle(java.lang.String title)
-  {
-    this._title = title;
-  } //-- void setTitle(java.lang.String)
-
-  /**
-   * Sets the value of field 'width'.
-   *
-   * @param width the value of field 'width'.
-   */
-  public void setWidth(int width)
-  {
-    this._width = width;
-    this._has_width = true;
-  } //-- void setWidth(int)
-
-  /**
-   * Sets the value of field 'wrapAlignment'.
-   *
-   * @param wrapAlignment the value of field 'wrapAlignment'.
-   */
-  public void setWrapAlignment(boolean wrapAlignment)
-  {
-    this._wrapAlignment = wrapAlignment;
-    this._has_wrapAlignment = true;
-  } //-- void setWrapAlignment(boolean)
-
-  /**
-   * Sets the value of field 'xpos'.
-   *
-   * @param xpos the value of field 'xpos'.
-   */
-  public void setXpos(int xpos)
-  {
-    this._xpos = xpos;
-    this._has_xpos = true;
-  } //-- void setXpos(int)
-
-  /**
-   * Sets the value of field 'ypos'.
-   *
-   * @param ypos the value of field 'ypos'.
-   */
-  public void setYpos(int ypos)
-  {
-    this._ypos = ypos;
-    this._has_ypos = true;
-  } //-- void setYpos(int)
-
-  /**
-   * Method unmarshal
-   *
-   *
-   *
-   * @param reader
-   * @return Object
-   */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.
-        Viewport.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 Viewport implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _conservationSelected
+     */
+    private boolean _conservationSelected;
+
+    /**
+     * keeps track of state for field: _conservationSelected
+     */
+    private boolean _has_conservationSelected;
+
+    /**
+     * Field _pidSelected
+     */
+    private boolean _pidSelected;
+
+    /**
+     * keeps track of state for field: _pidSelected
+     */
+    private boolean _has_pidSelected;
+
+    /**
+     * Field _bgColour
+     */
+    private java.lang.String _bgColour;
+
+    /**
+     * 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 _title
+     */
+    private java.lang.String _title;
+
+    /**
+     * Field _showFullId
+     */
+    private boolean _showFullId;
+
+    /**
+     * keeps track of state for field: _showFullId
+     */
+    private boolean _has_showFullId;
+
+    /**
+     * Field _showText
+     */
+    private boolean _showText;
+
+    /**
+     * keeps track of state for field: _showText
+     */
+    private boolean _has_showText;
+
+    /**
+     * Field _showColourText
+     */
+    private boolean _showColourText;
+
+    /**
+     * keeps track of state for field: _showColourText
+     */
+    private boolean _has_showColourText;
+
+    /**
+     * Field _showBoxes
+     */
+    private boolean _showBoxes;
+
+    /**
+     * keeps track of state for field: _showBoxes
+     */
+    private boolean _has_showBoxes;
+
+    /**
+     * Field _wrapAlignment
+     */
+    private boolean _wrapAlignment;
+
+    /**
+     * keeps track of state for field: _wrapAlignment
+     */
+    private boolean _has_wrapAlignment;
+
+    /**
+     * Field _renderGaps
+     */
+    private boolean _renderGaps;
+
+    /**
+     * keeps track of state for field: _renderGaps
+     */
+    private boolean _has_renderGaps;
+
+    /**
+     * Field _showSequenceFeatures
+     */
+    private boolean _showSequenceFeatures;
+
+    /**
+     * keeps track of state for field: _showSequenceFeatures
+     */
+    private boolean _has_showSequenceFeatures;
+
+    /**
+     * Field _showAnnotation
+     */
+    private boolean _showAnnotation;
+
+    /**
+     * keeps track of state for field: _showAnnotation
+     */
+    private boolean _has_showAnnotation;
+
+    /**
+     * Field _showConservation
+     */
+    private boolean _showConservation;
+
+    /**
+     * keeps track of state for field: _showConservation
+     */
+    private boolean _has_showConservation;
+
+    /**
+     * Field _showQuality
+     */
+    private boolean _showQuality;
+
+    /**
+     * keeps track of state for field: _showQuality
+     */
+    private boolean _has_showQuality;
+
+    /**
+     * Field _showIdentity
+     */
+    private boolean _showIdentity;
+
+    /**
+     * keeps track of state for field: _showIdentity
+     */
+    private boolean _has_showIdentity;
+
+    /**
+     * Field _xpos
+     */
+    private int _xpos;
+
+    /**
+     * keeps track of state for field: _xpos
+     */
+    private boolean _has_xpos;
+
+    /**
+     * Field _ypos
+     */
+    private int _ypos;
+
+    /**
+     * keeps track of state for field: _ypos
+     */
+    private boolean _has_ypos;
+
+    /**
+     * Field _width
+     */
+    private int _width;
+
+    /**
+     * keeps track of state for field: _width
+     */
+    private boolean _has_width;
+
+    /**
+     * Field _height
+     */
+    private int _height;
+
+    /**
+     * keeps track of state for field: _height
+     */
+    private boolean _has_height;
+
+    /**
+     * Field _startRes
+     */
+    private int _startRes;
+
+    /**
+     * keeps track of state for field: _startRes
+     */
+    private boolean _has_startRes;
+
+    /**
+     * Field _startSeq
+     */
+    private int _startSeq;
+
+    /**
+     * keeps track of state for field: _startSeq
+     */
+    private boolean _has_startSeq;
+
+    /**
+     * Field _fontName
+     */
+    private java.lang.String _fontName;
+
+    /**
+     * Field _fontSize
+     */
+    private int _fontSize;
+
+    /**
+     * keeps track of state for field: _fontSize
+     */
+    private boolean _has_fontSize;
+
+    /**
+     * Field _fontStyle
+     */
+    private int _fontStyle;
+
+    /**
+     * keeps track of state for field: _fontStyle
+     */
+    private boolean _has_fontStyle;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Viewport() {
+        super();
+    } //-- jalview.binding.Viewport()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteConsThreshold
+     * 
+     */
+    public void deleteConsThreshold()
+    {
+        this._has_consThreshold= false;
+    } //-- void deleteConsThreshold() 
+
+    /**
+     * Method deleteConservationSelected
+     * 
+     */
+    public void deleteConservationSelected()
+    {
+        this._has_conservationSelected= false;
+    } //-- void deleteConservationSelected() 
+
+    /**
+     * Method deleteFontSize
+     * 
+     */
+    public void deleteFontSize()
+    {
+        this._has_fontSize= false;
+    } //-- void deleteFontSize() 
+
+    /**
+     * Method deleteFontStyle
+     * 
+     */
+    public void deleteFontStyle()
+    {
+        this._has_fontStyle= false;
+    } //-- void deleteFontStyle() 
+
+    /**
+     * Method deleteHeight
+     * 
+     */
+    public void deleteHeight()
+    {
+        this._has_height= false;
+    } //-- void deleteHeight() 
+
+    /**
+     * Method deletePidSelected
+     * 
+     */
+    public void deletePidSelected()
+    {
+        this._has_pidSelected= false;
+    } //-- void deletePidSelected() 
+
+    /**
+     * Method deletePidThreshold
+     * 
+     */
+    public void deletePidThreshold()
+    {
+        this._has_pidThreshold= false;
+    } //-- void deletePidThreshold() 
+
+    /**
+     * Method deleteRenderGaps
+     * 
+     */
+    public void deleteRenderGaps()
+    {
+        this._has_renderGaps= false;
+    } //-- void deleteRenderGaps() 
+
+    /**
+     * Method deleteShowAnnotation
+     * 
+     */
+    public void deleteShowAnnotation()
+    {
+        this._has_showAnnotation= false;
+    } //-- void deleteShowAnnotation() 
+
+    /**
+     * Method deleteShowBoxes
+     * 
+     */
+    public void deleteShowBoxes()
+    {
+        this._has_showBoxes= false;
+    } //-- void deleteShowBoxes() 
+
+    /**
+     * Method deleteShowColourText
+     * 
+     */
+    public void deleteShowColourText()
+    {
+        this._has_showColourText= false;
+    } //-- void deleteShowColourText() 
+
+    /**
+     * Method deleteShowConservation
+     * 
+     */
+    public void deleteShowConservation()
+    {
+        this._has_showConservation= false;
+    } //-- void deleteShowConservation() 
+
+    /**
+     * Method deleteShowFullId
+     * 
+     */
+    public void deleteShowFullId()
+    {
+        this._has_showFullId= false;
+    } //-- void deleteShowFullId() 
+
+    /**
+     * Method deleteShowIdentity
+     * 
+     */
+    public void deleteShowIdentity()
+    {
+        this._has_showIdentity= false;
+    } //-- void deleteShowIdentity() 
+
+    /**
+     * Method deleteShowQuality
+     * 
+     */
+    public void deleteShowQuality()
+    {
+        this._has_showQuality= false;
+    } //-- void deleteShowQuality() 
+
+    /**
+     * Method deleteShowSequenceFeatures
+     * 
+     */
+    public void deleteShowSequenceFeatures()
+    {
+        this._has_showSequenceFeatures= false;
+    } //-- void deleteShowSequenceFeatures() 
+
+    /**
+     * Method deleteShowText
+     * 
+     */
+    public void deleteShowText()
+    {
+        this._has_showText= false;
+    } //-- void deleteShowText() 
+
+    /**
+     * Method deleteStartRes
+     * 
+     */
+    public void deleteStartRes()
+    {
+        this._has_startRes= false;
+    } //-- void deleteStartRes() 
+
+    /**
+     * Method deleteStartSeq
+     * 
+     */
+    public void deleteStartSeq()
+    {
+        this._has_startSeq= false;
+    } //-- void deleteStartSeq() 
+
+    /**
+     * Method deleteWidth
+     * 
+     */
+    public void deleteWidth()
+    {
+        this._has_width= false;
+    } //-- void deleteWidth() 
+
+    /**
+     * Method deleteWrapAlignment
+     * 
+     */
+    public void deleteWrapAlignment()
+    {
+        this._has_wrapAlignment= false;
+    } //-- void deleteWrapAlignment() 
+
+    /**
+     * Method deleteXpos
+     * 
+     */
+    public void deleteXpos()
+    {
+        this._has_xpos= false;
+    } //-- void deleteXpos() 
+
+    /**
+     * Method deleteYpos
+     * 
+     */
+    public void deleteYpos()
+    {
+        this._has_ypos= false;
+    } //-- void deleteYpos() 
+
+    /**
+     * Returns the value of field 'bgColour'.
+     * 
+     * @return String
+     * @return the value of field 'bgColour'.
+     */
+    public java.lang.String getBgColour()
+    {
+        return this._bgColour;
+    } //-- java.lang.String getBgColour() 
+
+    /**
+     * 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 'conservationSelected'.
+     * 
+     * @return boolean
+     * @return the value of field 'conservationSelected'.
+     */
+    public boolean getConservationSelected()
+    {
+        return this._conservationSelected;
+    } //-- boolean getConservationSelected() 
+
+    /**
+     * Returns the value of field 'fontName'.
+     * 
+     * @return String
+     * @return the value of field 'fontName'.
+     */
+    public java.lang.String getFontName()
+    {
+        return this._fontName;
+    } //-- java.lang.String getFontName() 
+
+    /**
+     * Returns the value of field 'fontSize'.
+     * 
+     * @return int
+     * @return the value of field 'fontSize'.
+     */
+    public int getFontSize()
+    {
+        return this._fontSize;
+    } //-- int getFontSize() 
+
+    /**
+     * Returns the value of field 'fontStyle'.
+     * 
+     * @return int
+     * @return the value of field 'fontStyle'.
+     */
+    public int getFontStyle()
+    {
+        return this._fontStyle;
+    } //-- int getFontStyle() 
+
+    /**
+     * Returns the value of field 'height'.
+     * 
+     * @return int
+     * @return the value of field 'height'.
+     */
+    public int getHeight()
+    {
+        return this._height;
+    } //-- int getHeight() 
+
+    /**
+     * Returns the value of field 'pidSelected'.
+     * 
+     * @return boolean
+     * @return the value of field 'pidSelected'.
+     */
+    public boolean getPidSelected()
+    {
+        return this._pidSelected;
+    } //-- boolean getPidSelected() 
+
+    /**
+     * Returns the value of field 'pidThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'pidThreshold'.
+     */
+    public int getPidThreshold()
+    {
+        return this._pidThreshold;
+    } //-- int getPidThreshold() 
+
+    /**
+     * Returns the value of field 'renderGaps'.
+     * 
+     * @return boolean
+     * @return the value of field 'renderGaps'.
+     */
+    public boolean getRenderGaps()
+    {
+        return this._renderGaps;
+    } //-- boolean getRenderGaps() 
+
+    /**
+     * Returns the value of field 'showAnnotation'.
+     * 
+     * @return boolean
+     * @return the value of field 'showAnnotation'.
+     */
+    public boolean getShowAnnotation()
+    {
+        return this._showAnnotation;
+    } //-- boolean getShowAnnotation() 
+
+    /**
+     * Returns the value of field 'showBoxes'.
+     * 
+     * @return boolean
+     * @return the value of field 'showBoxes'.
+     */
+    public boolean getShowBoxes()
+    {
+        return this._showBoxes;
+    } //-- boolean getShowBoxes() 
+
+    /**
+     * Returns the value of field 'showColourText'.
+     * 
+     * @return boolean
+     * @return the value of field 'showColourText'.
+     */
+    public boolean getShowColourText()
+    {
+        return this._showColourText;
+    } //-- boolean getShowColourText() 
+
+    /**
+     * Returns the value of field 'showConservation'.
+     * 
+     * @return boolean
+     * @return the value of field 'showConservation'.
+     */
+    public boolean getShowConservation()
+    {
+        return this._showConservation;
+    } //-- boolean getShowConservation() 
+
+    /**
+     * Returns the value of field 'showFullId'.
+     * 
+     * @return boolean
+     * @return the value of field 'showFullId'.
+     */
+    public boolean getShowFullId()
+    {
+        return this._showFullId;
+    } //-- boolean getShowFullId() 
+
+    /**
+     * Returns the value of field 'showIdentity'.
+     * 
+     * @return boolean
+     * @return the value of field 'showIdentity'.
+     */
+    public boolean getShowIdentity()
+    {
+        return this._showIdentity;
+    } //-- boolean getShowIdentity() 
+
+    /**
+     * Returns the value of field 'showQuality'.
+     * 
+     * @return boolean
+     * @return the value of field 'showQuality'.
+     */
+    public boolean getShowQuality()
+    {
+        return this._showQuality;
+    } //-- boolean getShowQuality() 
+
+    /**
+     * Returns the value of field 'showSequenceFeatures'.
+     * 
+     * @return boolean
+     * @return the value of field 'showSequenceFeatures'.
+     */
+    public boolean getShowSequenceFeatures()
+    {
+        return this._showSequenceFeatures;
+    } //-- boolean getShowSequenceFeatures() 
+
+    /**
+     * Returns the value of field 'showText'.
+     * 
+     * @return boolean
+     * @return the value of field 'showText'.
+     */
+    public boolean getShowText()
+    {
+        return this._showText;
+    } //-- boolean getShowText() 
+
+    /**
+     * Returns the value of field 'startRes'.
+     * 
+     * @return int
+     * @return the value of field 'startRes'.
+     */
+    public int getStartRes()
+    {
+        return this._startRes;
+    } //-- int getStartRes() 
+
+    /**
+     * Returns the value of field 'startSeq'.
+     * 
+     * @return int
+     * @return the value of field 'startSeq'.
+     */
+    public int getStartSeq()
+    {
+        return this._startSeq;
+    } //-- int getStartSeq() 
+
+    /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
+     * Returns the value of field 'width'.
+     * 
+     * @return int
+     * @return the value of field 'width'.
+     */
+    public int getWidth()
+    {
+        return this._width;
+    } //-- int getWidth() 
+
+    /**
+     * Returns the value of field 'wrapAlignment'.
+     * 
+     * @return boolean
+     * @return the value of field 'wrapAlignment'.
+     */
+    public boolean getWrapAlignment()
+    {
+        return this._wrapAlignment;
+    } //-- boolean getWrapAlignment() 
+
+    /**
+     * Returns the value of field 'xpos'.
+     * 
+     * @return int
+     * @return the value of field 'xpos'.
+     */
+    public int getXpos()
+    {
+        return this._xpos;
+    } //-- int getXpos() 
+
+    /**
+     * Returns the value of field 'ypos'.
+     * 
+     * @return int
+     * @return the value of field 'ypos'.
+     */
+    public int getYpos()
+    {
+        return this._ypos;
+    } //-- int getYpos() 
+
+    /**
+     * Method hasConsThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConsThreshold()
+    {
+        return this._has_consThreshold;
+    } //-- boolean hasConsThreshold() 
+
+    /**
+     * Method hasConservationSelected
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConservationSelected()
+    {
+        return this._has_conservationSelected;
+    } //-- boolean hasConservationSelected() 
+
+    /**
+     * Method hasFontSize
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontSize()
+    {
+        return this._has_fontSize;
+    } //-- boolean hasFontSize() 
+
+    /**
+     * Method hasFontStyle
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontStyle()
+    {
+        return this._has_fontStyle;
+    } //-- boolean hasFontStyle() 
+
+    /**
+     * Method hasHeight
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasHeight()
+    {
+        return this._has_height;
+    } //-- boolean hasHeight() 
+
+    /**
+     * Method hasPidSelected
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidSelected()
+    {
+        return this._has_pidSelected;
+    } //-- boolean hasPidSelected() 
+
+    /**
+     * Method hasPidThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidThreshold()
+    {
+        return this._has_pidThreshold;
+    } //-- boolean hasPidThreshold() 
+
+    /**
+     * Method hasRenderGaps
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasRenderGaps()
+    {
+        return this._has_renderGaps;
+    } //-- boolean hasRenderGaps() 
+
+    /**
+     * Method hasShowAnnotation
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowAnnotation()
+    {
+        return this._has_showAnnotation;
+    } //-- boolean hasShowAnnotation() 
+
+    /**
+     * Method hasShowBoxes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowBoxes()
+    {
+        return this._has_showBoxes;
+    } //-- boolean hasShowBoxes() 
+
+    /**
+     * Method hasShowColourText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowColourText()
+    {
+        return this._has_showColourText;
+    } //-- boolean hasShowColourText() 
+
+    /**
+     * Method hasShowConservation
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowConservation()
+    {
+        return this._has_showConservation;
+    } //-- boolean hasShowConservation() 
+
+    /**
+     * Method hasShowFullId
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowFullId()
+    {
+        return this._has_showFullId;
+    } //-- boolean hasShowFullId() 
+
+    /**
+     * Method hasShowIdentity
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowIdentity()
+    {
+        return this._has_showIdentity;
+    } //-- boolean hasShowIdentity() 
+
+    /**
+     * Method hasShowQuality
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowQuality()
+    {
+        return this._has_showQuality;
+    } //-- boolean hasShowQuality() 
+
+    /**
+     * Method hasShowSequenceFeatures
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowSequenceFeatures()
+    {
+        return this._has_showSequenceFeatures;
+    } //-- boolean hasShowSequenceFeatures() 
+
+    /**
+     * Method hasShowText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowText()
+    {
+        return this._has_showText;
+    } //-- boolean hasShowText() 
+
+    /**
+     * Method hasStartRes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStartRes()
+    {
+        return this._has_startRes;
+    } //-- boolean hasStartRes() 
+
+    /**
+     * Method hasStartSeq
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStartSeq()
+    {
+        return this._has_startSeq;
+    } //-- boolean hasStartSeq() 
+
+    /**
+     * Method hasWidth
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasWidth()
+    {
+        return this._has_width;
+    } //-- boolean hasWidth() 
+
+    /**
+     * Method hasWrapAlignment
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasWrapAlignment()
+    {
+        return this._has_wrapAlignment;
+    } //-- boolean hasWrapAlignment() 
+
+    /**
+     * Method hasXpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasXpos()
+    {
+        return this._has_xpos;
+    } //-- boolean hasXpos() 
+
+    /**
+     * Method hasYpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasYpos()
+    {
+        return this._has_ypos;
+    } //-- boolean hasYpos() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'bgColour'.
+     * 
+     * @param bgColour the value of field 'bgColour'.
+     */
+    public void setBgColour(java.lang.String bgColour)
+    {
+        this._bgColour = bgColour;
+    } //-- void setBgColour(java.lang.String) 
+
+    /**
+     * 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 'conservationSelected'.
+     * 
+     * @param conservationSelected the value of field
+     * 'conservationSelected'.
+     */
+    public void setConservationSelected(boolean conservationSelected)
+    {
+        this._conservationSelected = conservationSelected;
+        this._has_conservationSelected = true;
+    } //-- void setConservationSelected(boolean) 
+
+    /**
+     * Sets the value of field 'fontName'.
+     * 
+     * @param fontName the value of field 'fontName'.
+     */
+    public void setFontName(java.lang.String fontName)
+    {
+        this._fontName = fontName;
+    } //-- void setFontName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'fontSize'.
+     * 
+     * @param fontSize the value of field 'fontSize'.
+     */
+    public void setFontSize(int fontSize)
+    {
+        this._fontSize = fontSize;
+        this._has_fontSize = true;
+    } //-- void setFontSize(int) 
+
+    /**
+     * Sets the value of field 'fontStyle'.
+     * 
+     * @param fontStyle the value of field 'fontStyle'.
+     */
+    public void setFontStyle(int fontStyle)
+    {
+        this._fontStyle = fontStyle;
+        this._has_fontStyle = true;
+    } //-- void setFontStyle(int) 
+
+    /**
+     * Sets the value of field 'height'.
+     * 
+     * @param height the value of field 'height'.
+     */
+    public void setHeight(int height)
+    {
+        this._height = height;
+        this._has_height = true;
+    } //-- void setHeight(int) 
+
+    /**
+     * Sets the value of field 'pidSelected'.
+     * 
+     * @param pidSelected the value of field 'pidSelected'.
+     */
+    public void setPidSelected(boolean pidSelected)
+    {
+        this._pidSelected = pidSelected;
+        this._has_pidSelected = true;
+    } //-- void setPidSelected(boolean) 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'renderGaps'.
+     * 
+     * @param renderGaps the value of field 'renderGaps'.
+     */
+    public void setRenderGaps(boolean renderGaps)
+    {
+        this._renderGaps = renderGaps;
+        this._has_renderGaps = true;
+    } //-- void setRenderGaps(boolean) 
+
+    /**
+     * Sets the value of field 'showAnnotation'.
+     * 
+     * @param showAnnotation the value of field 'showAnnotation'.
+     */
+    public void setShowAnnotation(boolean showAnnotation)
+    {
+        this._showAnnotation = showAnnotation;
+        this._has_showAnnotation = true;
+    } //-- void setShowAnnotation(boolean) 
+
+    /**
+     * Sets the value of field 'showBoxes'.
+     * 
+     * @param showBoxes the value of field 'showBoxes'.
+     */
+    public void setShowBoxes(boolean showBoxes)
+    {
+        this._showBoxes = showBoxes;
+        this._has_showBoxes = true;
+    } //-- void setShowBoxes(boolean) 
+
+    /**
+     * Sets the value of field 'showColourText'.
+     * 
+     * @param showColourText the value of field 'showColourText'.
+     */
+    public void setShowColourText(boolean showColourText)
+    {
+        this._showColourText = showColourText;
+        this._has_showColourText = true;
+    } //-- void setShowColourText(boolean) 
+
+    /**
+     * Sets the value of field 'showConservation'.
+     * 
+     * @param showConservation the value of field 'showConservation'
+     */
+    public void setShowConservation(boolean showConservation)
+    {
+        this._showConservation = showConservation;
+        this._has_showConservation = true;
+    } //-- void setShowConservation(boolean) 
+
+    /**
+     * Sets the value of field 'showFullId'.
+     * 
+     * @param showFullId the value of field 'showFullId'.
+     */
+    public void setShowFullId(boolean showFullId)
+    {
+        this._showFullId = showFullId;
+        this._has_showFullId = true;
+    } //-- void setShowFullId(boolean) 
+
+    /**
+     * Sets the value of field 'showIdentity'.
+     * 
+     * @param showIdentity the value of field 'showIdentity'.
+     */
+    public void setShowIdentity(boolean showIdentity)
+    {
+        this._showIdentity = showIdentity;
+        this._has_showIdentity = true;
+    } //-- void setShowIdentity(boolean) 
+
+    /**
+     * Sets the value of field 'showQuality'.
+     * 
+     * @param showQuality the value of field 'showQuality'.
+     */
+    public void setShowQuality(boolean showQuality)
+    {
+        this._showQuality = showQuality;
+        this._has_showQuality = true;
+    } //-- void setShowQuality(boolean) 
+
+    /**
+     * Sets the value of field 'showSequenceFeatures'.
+     * 
+     * @param showSequenceFeatures the value of field
+     * 'showSequenceFeatures'.
+     */
+    public void setShowSequenceFeatures(boolean showSequenceFeatures)
+    {
+        this._showSequenceFeatures = showSequenceFeatures;
+        this._has_showSequenceFeatures = true;
+    } //-- void setShowSequenceFeatures(boolean) 
+
+    /**
+     * Sets the value of field 'showText'.
+     * 
+     * @param showText the value of field 'showText'.
+     */
+    public void setShowText(boolean showText)
+    {
+        this._showText = showText;
+        this._has_showText = true;
+    } //-- void setShowText(boolean) 
+
+    /**
+     * Sets the value of field 'startRes'.
+     * 
+     * @param startRes the value of field 'startRes'.
+     */
+    public void setStartRes(int startRes)
+    {
+        this._startRes = startRes;
+        this._has_startRes = true;
+    } //-- void setStartRes(int) 
+
+    /**
+     * Sets the value of field 'startSeq'.
+     * 
+     * @param startSeq the value of field 'startSeq'.
+     */
+    public void setStartSeq(int startSeq)
+    {
+        this._startSeq = startSeq;
+        this._has_startSeq = true;
+    } //-- void setStartSeq(int) 
+
+    /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
+     * Sets the value of field 'width'.
+     * 
+     * @param width the value of field 'width'.
+     */
+    public void setWidth(int width)
+    {
+        this._width = width;
+        this._has_width = true;
+    } //-- void setWidth(int) 
+
+    /**
+     * Sets the value of field 'wrapAlignment'.
+     * 
+     * @param wrapAlignment the value of field 'wrapAlignment'.
+     */
+    public void setWrapAlignment(boolean wrapAlignment)
+    {
+        this._wrapAlignment = wrapAlignment;
+        this._has_wrapAlignment = true;
+    } //-- void setWrapAlignment(boolean) 
+
+    /**
+     * Sets the value of field 'xpos'.
+     * 
+     * @param xpos the value of field 'xpos'.
+     */
+    public void setXpos(int xpos)
+    {
+        this._xpos = xpos;
+        this._has_xpos = true;
+    } //-- void setXpos(int) 
+
+    /**
+     * Sets the value of field 'ypos'.
+     * 
+     * @param ypos the value of field 'ypos'.
+     */
+    public void setYpos(int ypos)
+    {
+        this._ypos = ypos;
+        this._has_ypos = true;
+    } //-- void setYpos(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.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() 
 
 }