X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=d212e84fae0f4208afbedab0062a18e0c58f8ec5;hb=cfa1e4489edf808823a672584fe41084cb33b00f;hp=6dfb14fe72e32b8abffc2eea44308318ad127d70;hpb=8c4f77adba0521e7dc89dcb77fe2f8b28c62f70d;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 6dfb14f..d212e84 100755
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,6 +1,6 @@
 /*
  * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
  * Schema.
  * $Id$
  */
@@ -11,17 +11,8 @@ package jalview.schemabinding.version2;
  //- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
 
 /**
  * Class Viewport.
@@ -36,7 +27,7 @@ public class Viewport implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _conservationSelected
+     * Field _conservationSelected.
      */
     private boolean _conservationSelected;
 
@@ -46,7 +37,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_conservationSelected;
 
     /**
-     * Field _pidSelected
+     * Field _pidSelected.
      */
     private boolean _pidSelected;
 
@@ -56,12 +47,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_pidSelected;
 
     /**
-     * Field _bgColour
+     * Field _bgColour.
      */
     private java.lang.String _bgColour;
 
     /**
-     * Field _consThreshold
+     * Field _consThreshold.
      */
     private int _consThreshold;
 
@@ -71,7 +62,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_consThreshold;
 
     /**
-     * Field _pidThreshold
+     * Field _pidThreshold.
      */
     private int _pidThreshold;
 
@@ -81,12 +72,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_pidThreshold;
 
     /**
-     * Field _title
+     * Field _title.
      */
     private java.lang.String _title;
 
     /**
-     * Field _showFullId
+     * Field _showFullId.
      */
     private boolean _showFullId;
 
@@ -96,7 +87,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showFullId;
 
     /**
-     * Field _rightAlignIds
+     * Field _rightAlignIds.
      */
     private boolean _rightAlignIds;
 
@@ -106,7 +97,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_rightAlignIds;
 
     /**
-     * Field _showText
+     * Field _showText.
      */
     private boolean _showText;
 
@@ -116,7 +107,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showText;
 
     /**
-     * Field _showColourText
+     * Field _showColourText.
      */
     private boolean _showColourText;
 
@@ -126,7 +117,17 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showColourText;
 
     /**
-     * Field _showBoxes
+     * Field _showUnconserved.
+     */
+    private boolean _showUnconserved;
+
+    /**
+     * keeps track of state for field: _showUnconserved
+     */
+    private boolean _has_showUnconserved;
+
+    /**
+     * Field _showBoxes.
      */
     private boolean _showBoxes;
 
@@ -136,7 +137,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showBoxes;
 
     /**
-     * Field _wrapAlignment
+     * Field _wrapAlignment.
      */
     private boolean _wrapAlignment;
 
@@ -146,7 +147,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_wrapAlignment;
 
     /**
-     * Field _renderGaps
+     * Field _renderGaps.
      */
     private boolean _renderGaps;
 
@@ -156,7 +157,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_renderGaps;
 
     /**
-     * Field _showSequenceFeatures
+     * Field _showSequenceFeatures.
      */
     private boolean _showSequenceFeatures;
 
@@ -166,7 +167,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showSequenceFeatures;
 
     /**
-     * Field _showAnnotation
+     * Field _showAnnotation.
      */
     private boolean _showAnnotation;
 
@@ -176,7 +177,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showAnnotation;
 
     /**
-     * Field _xpos
+     * Field _xpos.
      */
     private int _xpos;
 
@@ -186,7 +187,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_xpos;
 
     /**
-     * Field _ypos
+     * Field _ypos.
      */
     private int _ypos;
 
@@ -196,7 +197,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_ypos;
 
     /**
-     * Field _width
+     * Field _width.
      */
     private int _width;
 
@@ -206,7 +207,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_width;
 
     /**
-     * Field _height
+     * Field _height.
      */
     private int _height;
 
@@ -216,7 +217,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_height;
 
     /**
-     * Field _startRes
+     * Field _startRes.
      */
     private int _startRes;
 
@@ -226,7 +227,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_startRes;
 
     /**
-     * Field _startSeq
+     * Field _startSeq.
      */
     private int _startSeq;
 
@@ -236,12 +237,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_startSeq;
 
     /**
-     * Field _fontName
+     * Field _fontName.
      */
     private java.lang.String _fontName;
 
     /**
-     * Field _fontSize
+     * Field _fontSize.
      */
     private int _fontSize;
 
@@ -251,7 +252,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontSize;
 
     /**
-     * Field _fontStyle
+     * Field _fontStyle.
      */
     private int _fontStyle;
 
@@ -261,17 +262,17 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontStyle;
 
     /**
-     * Field _viewName
+     * Field _viewName.
      */
     private java.lang.String _viewName;
 
     /**
-     * Field _sequenceSetId
+     * Field _sequenceSetId.
      */
     private java.lang.String _sequenceSetId;
 
     /**
-     * Field _gatheredViews
+     * Field _gatheredViews.
      */
     private boolean _gatheredViews;
 
@@ -281,7 +282,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_gatheredViews;
 
     /**
-     * Field _textCol1
+     * Field _textCol1.
      */
     private int _textCol1;
 
@@ -291,7 +292,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_textCol1;
 
     /**
-     * Field _textCol2
+     * Field _textCol2.
      */
     private int _textCol2;
 
@@ -301,7 +302,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_textCol2;
 
     /**
-     * Field _textColThreshold
+     * Field _textColThreshold.
      */
     private int _textColThreshold;
 
@@ -311,12 +312,19 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_textColThreshold;
 
     /**
-     * Field _annotationColours
+     * unique id used by jalview to synchronize between stored and
+     * instantiated views
+     *  
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _annotationColours.
      */
     private jalview.schemabinding.version2.AnnotationColours _annotationColours;
 
     /**
-     * Field _hiddenColumnsList
+     * Field _hiddenColumnsList.
      */
     private java.util.Vector _hiddenColumnsList;
 
@@ -327,8 +335,8 @@ public class Viewport implements java.io.Serializable {
 
     public Viewport() {
         super();
-        _hiddenColumnsList = new Vector();
-    } //-- jalview.schemabinding.version2.Viewport()
+        this._hiddenColumnsList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -336,1027 +344,1075 @@ public class Viewport implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addHiddenColumns
-     * 
      * 
      * 
      * @param vHiddenColumns
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenColumnsList.addElement(vHiddenColumns);
-    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
+    public void addHiddenColumns(
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenColumnsList.addElement(vHiddenColumns);
+    }
 
     /**
-     * Method addHiddenColumns
-     * 
      * 
      * 
      * @param index
      * @param vHiddenColumns
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
-    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
+    public void addHiddenColumns(
+            final int index,
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenColumnsList.add(index, vHiddenColumns);
+    }
 
     /**
-     * Method deleteConsThreshold
-     * 
      */
-    public void deleteConsThreshold()
-    {
+    public void deleteConsThreshold(
+    ) {
         this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
+    }
 
     /**
-     * Method deleteConservationSelected
-     * 
      */
-    public void deleteConservationSelected()
-    {
+    public void deleteConservationSelected(
+    ) {
         this._has_conservationSelected= false;
-    } //-- void deleteConservationSelected() 
+    }
 
     /**
-     * Method deleteFontSize
-     * 
      */
-    public void deleteFontSize()
-    {
+    public void deleteFontSize(
+    ) {
         this._has_fontSize= false;
-    } //-- void deleteFontSize() 
+    }
 
     /**
-     * Method deleteFontStyle
-     * 
      */
-    public void deleteFontStyle()
-    {
+    public void deleteFontStyle(
+    ) {
         this._has_fontStyle= false;
-    } //-- void deleteFontStyle() 
+    }
 
     /**
-     * Method deleteGatheredViews
-     * 
      */
-    public void deleteGatheredViews()
-    {
+    public void deleteGatheredViews(
+    ) {
         this._has_gatheredViews= false;
-    } //-- void deleteGatheredViews() 
+    }
 
     /**
-     * Method deleteHeight
-     * 
      */
-    public void deleteHeight()
-    {
+    public void deleteHeight(
+    ) {
         this._has_height= false;
-    } //-- void deleteHeight() 
+    }
 
     /**
-     * Method deletePidSelected
-     * 
      */
-    public void deletePidSelected()
-    {
+    public void deletePidSelected(
+    ) {
         this._has_pidSelected= false;
-    } //-- void deletePidSelected() 
+    }
 
     /**
-     * Method deletePidThreshold
-     * 
      */
-    public void deletePidThreshold()
-    {
+    public void deletePidThreshold(
+    ) {
         this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
+    }
 
     /**
-     * Method deleteRenderGaps
-     * 
      */
-    public void deleteRenderGaps()
-    {
+    public void deleteRenderGaps(
+    ) {
         this._has_renderGaps= false;
-    } //-- void deleteRenderGaps() 
+    }
 
     /**
-     * Method deleteRightAlignIds
-     * 
      */
-    public void deleteRightAlignIds()
-    {
+    public void deleteRightAlignIds(
+    ) {
         this._has_rightAlignIds= false;
-    } //-- void deleteRightAlignIds() 
+    }
 
     /**
-     * Method deleteShowAnnotation
-     * 
      */
-    public void deleteShowAnnotation()
-    {
+    public void deleteShowAnnotation(
+    ) {
         this._has_showAnnotation= false;
-    } //-- void deleteShowAnnotation() 
+    }
 
     /**
-     * Method deleteShowBoxes
-     * 
      */
-    public void deleteShowBoxes()
-    {
+    public void deleteShowBoxes(
+    ) {
         this._has_showBoxes= false;
-    } //-- void deleteShowBoxes() 
+    }
 
     /**
-     * Method deleteShowColourText
-     * 
      */
-    public void deleteShowColourText()
-    {
+    public void deleteShowColourText(
+    ) {
         this._has_showColourText= false;
-    } //-- void deleteShowColourText() 
+    }
 
     /**
-     * Method deleteShowFullId
-     * 
      */
-    public void deleteShowFullId()
-    {
+    public void deleteShowFullId(
+    ) {
         this._has_showFullId= false;
-    } //-- void deleteShowFullId() 
+    }
 
     /**
-     * Method deleteShowSequenceFeatures
-     * 
      */
-    public void deleteShowSequenceFeatures()
-    {
+    public void deleteShowSequenceFeatures(
+    ) {
         this._has_showSequenceFeatures= false;
-    } //-- void deleteShowSequenceFeatures() 
+    }
 
     /**
-     * Method deleteShowText
-     * 
      */
-    public void deleteShowText()
-    {
+    public void deleteShowText(
+    ) {
         this._has_showText= false;
-    } //-- void deleteShowText() 
+    }
 
     /**
-     * Method deleteStartRes
-     * 
      */
-    public void deleteStartRes()
-    {
+    public void deleteShowUnconserved(
+    ) {
+        this._has_showUnconserved= false;
+    }
+
+    /**
+     */
+    public void deleteStartRes(
+    ) {
         this._has_startRes= false;
-    } //-- void deleteStartRes() 
+    }
 
     /**
-     * Method deleteStartSeq
-     * 
      */
-    public void deleteStartSeq()
-    {
+    public void deleteStartSeq(
+    ) {
         this._has_startSeq= false;
-    } //-- void deleteStartSeq() 
+    }
 
     /**
-     * Method deleteTextCol1
-     * 
      */
-    public void deleteTextCol1()
-    {
+    public void deleteTextCol1(
+    ) {
         this._has_textCol1= false;
-    } //-- void deleteTextCol1() 
+    }
 
     /**
-     * Method deleteTextCol2
-     * 
      */
-    public void deleteTextCol2()
-    {
+    public void deleteTextCol2(
+    ) {
         this._has_textCol2= false;
-    } //-- void deleteTextCol2() 
+    }
 
     /**
-     * Method deleteTextColThreshold
-     * 
      */
-    public void deleteTextColThreshold()
-    {
+    public void deleteTextColThreshold(
+    ) {
         this._has_textColThreshold= false;
-    } //-- void deleteTextColThreshold() 
+    }
 
     /**
-     * Method deleteWidth
-     * 
      */
-    public void deleteWidth()
-    {
+    public void deleteWidth(
+    ) {
         this._has_width= false;
-    } //-- void deleteWidth() 
+    }
 
     /**
-     * Method deleteWrapAlignment
-     * 
      */
-    public void deleteWrapAlignment()
-    {
+    public void deleteWrapAlignment(
+    ) {
         this._has_wrapAlignment= false;
-    } //-- void deleteWrapAlignment() 
+    }
 
     /**
-     * Method deleteXpos
-     * 
      */
-    public void deleteXpos()
-    {
+    public void deleteXpos(
+    ) {
         this._has_xpos= false;
-    } //-- void deleteXpos() 
+    }
 
     /**
-     * Method deleteYpos
-     * 
      */
-    public void deleteYpos()
-    {
+    public void deleteYpos(
+    ) {
         this._has_ypos= false;
-    } //-- void deleteYpos() 
+    }
 
     /**
-     * Method enumerateHiddenColumns
-     * 
-     * 
+     * Method enumerateHiddenColumns.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.HiddenColumns elements
      */
-    public java.util.Enumeration enumerateHiddenColumns()
-    {
-        return _hiddenColumnsList.elements();
-    } //-- java.util.Enumeration enumerateHiddenColumns() 
+    public java.util.Enumeration enumerateHiddenColumns(
+    ) {
+        return this._hiddenColumnsList.elements();
+    }
 
     /**
      * Returns the value of field 'annotationColours'.
      * 
-     * @return AnnotationColours
-     * @return the value of field 'annotationColours'.
+     * @return the value of field 'AnnotationColours'.
      */
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
-    {
+    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
+    ) {
         return this._annotationColours;
-    } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() 
+    }
 
     /**
      * Returns the value of field 'bgColour'.
      * 
-     * @return String
-     * @return the value of field 'bgColour'.
+     * @return the value of field 'BgColour'.
      */
-    public java.lang.String getBgColour()
-    {
+    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'.
+     * @return the value of field 'ConsThreshold'.
      */
-    public int getConsThreshold()
-    {
+    public int getConsThreshold(
+    ) {
         return this._consThreshold;
-    } //-- int getConsThreshold() 
+    }
 
     /**
      * Returns the value of field 'conservationSelected'.
      * 
-     * @return boolean
-     * @return the value of field 'conservationSelected'.
+     * @return the value of field 'ConservationSelected'.
      */
-    public boolean getConservationSelected()
-    {
+    public boolean getConservationSelected(
+    ) {
         return this._conservationSelected;
-    } //-- boolean getConservationSelected() 
+    }
 
     /**
      * Returns the value of field 'fontName'.
      * 
-     * @return String
-     * @return the value of field 'fontName'.
+     * @return the value of field 'FontName'.
      */
-    public java.lang.String getFontName()
-    {
+    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'.
+     * @return the value of field 'FontSize'.
      */
-    public int getFontSize()
-    {
+    public int getFontSize(
+    ) {
         return this._fontSize;
-    } //-- int getFontSize() 
+    }
 
     /**
      * Returns the value of field 'fontStyle'.
      * 
-     * @return int
-     * @return the value of field 'fontStyle'.
+     * @return the value of field 'FontStyle'.
      */
-    public int getFontStyle()
-    {
+    public int getFontStyle(
+    ) {
         return this._fontStyle;
-    } //-- int getFontStyle() 
+    }
 
     /**
      * Returns the value of field 'gatheredViews'.
      * 
-     * @return boolean
-     * @return the value of field 'gatheredViews'.
+     * @return the value of field 'GatheredViews'.
      */
-    public boolean getGatheredViews()
-    {
+    public boolean getGatheredViews(
+    ) {
         return this._gatheredViews;
-    } //-- boolean getGatheredViews() 
+    }
 
     /**
      * Returns the value of field 'height'.
      * 
-     * @return int
-     * @return the value of field 'height'.
+     * @return the value of field 'Height'.
      */
-    public int getHeight()
-    {
+    public int getHeight(
+    ) {
         return this._height;
-    } //-- int getHeight() 
+    }
 
     /**
-     * Method getHiddenColumns
-     * 
-     * 
+     * Method getHiddenColumns.
      * 
      * @param index
-     * @return HiddenColumns
-     */
-    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.HiddenColumns at the given
+     * index
+     */
+    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenColumnsList.size()) {
+            throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
         }
         
-        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
-    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) 
+        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
+    }
 
     /**
-     * Method getHiddenColumns
-     * 
+     * Method getHiddenColumns.Returns the contents of the
+     * collection in an Array.  <p>Note:  Just in case the
+     * collection contents are changing in another thread, we pass
+     * a 0-length Array of the correct type into the API call. 
+     * This way we <i>know</i> that the Array returned is of
+     * exactly the correct length.
      * 
-     * 
-     * @return HiddenColumns
+     * @return this collection as an Array
      */
-    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
-    {
-        int size = _hiddenColumnsList.size();
-        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() 
+    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
+    ) {
+        jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+        return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
+    }
 
     /**
-     * Method getHiddenColumnsCount
-     * 
+     * Method getHiddenColumnsCount.
      * 
+     * @return the size of this collection
+     */
+    public int getHiddenColumnsCount(
+    ) {
+        return this._hiddenColumnsList.size();
+    }
+
+    /**
+     * Returns the value of field 'id'. The field 'id' has the
+     * following description: unique id used by jalview to
+     * synchronize between stored and instantiated views
+     *  
      * 
-     * @return int
+     * @return the value of field 'Id'.
      */
-    public int getHiddenColumnsCount()
-    {
-        return _hiddenColumnsList.size();
-    } //-- int getHiddenColumnsCount() 
+    public java.lang.String getId(
+    ) {
+        return this._id;
+    }
 
     /**
      * Returns the value of field 'pidSelected'.
      * 
-     * @return boolean
-     * @return the value of field 'pidSelected'.
+     * @return the value of field 'PidSelected'.
      */
-    public boolean getPidSelected()
-    {
+    public boolean getPidSelected(
+    ) {
         return this._pidSelected;
-    } //-- boolean getPidSelected() 
+    }
 
     /**
      * Returns the value of field 'pidThreshold'.
      * 
-     * @return int
-     * @return the value of field 'pidThreshold'.
+     * @return the value of field 'PidThreshold'.
      */
-    public int getPidThreshold()
-    {
+    public int getPidThreshold(
+    ) {
         return this._pidThreshold;
-    } //-- int getPidThreshold() 
+    }
 
     /**
      * Returns the value of field 'renderGaps'.
      * 
-     * @return boolean
-     * @return the value of field 'renderGaps'.
+     * @return the value of field 'RenderGaps'.
      */
-    public boolean getRenderGaps()
-    {
+    public boolean getRenderGaps(
+    ) {
         return this._renderGaps;
-    } //-- boolean getRenderGaps() 
+    }
 
     /**
      * Returns the value of field 'rightAlignIds'.
      * 
-     * @return boolean
-     * @return the value of field 'rightAlignIds'.
+     * @return the value of field 'RightAlignIds'.
      */
-    public boolean getRightAlignIds()
-    {
+    public boolean getRightAlignIds(
+    ) {
         return this._rightAlignIds;
-    } //-- boolean getRightAlignIds() 
+    }
 
     /**
      * Returns the value of field 'sequenceSetId'.
      * 
-     * @return String
-     * @return the value of field 'sequenceSetId'.
+     * @return the value of field 'SequenceSetId'.
      */
-    public java.lang.String getSequenceSetId()
-    {
+    public java.lang.String getSequenceSetId(
+    ) {
         return this._sequenceSetId;
-    } //-- java.lang.String getSequenceSetId() 
+    }
 
     /**
      * Returns the value of field 'showAnnotation'.
      * 
-     * @return boolean
-     * @return the value of field 'showAnnotation'.
+     * @return the value of field 'ShowAnnotation'.
      */
-    public boolean getShowAnnotation()
-    {
+    public boolean getShowAnnotation(
+    ) {
         return this._showAnnotation;
-    } //-- boolean getShowAnnotation() 
+    }
 
     /**
      * Returns the value of field 'showBoxes'.
      * 
-     * @return boolean
-     * @return the value of field 'showBoxes'.
+     * @return the value of field 'ShowBoxes'.
      */
-    public boolean getShowBoxes()
-    {
+    public boolean getShowBoxes(
+    ) {
         return this._showBoxes;
-    } //-- boolean getShowBoxes() 
+    }
 
     /**
      * Returns the value of field 'showColourText'.
      * 
-     * @return boolean
-     * @return the value of field 'showColourText'.
+     * @return the value of field 'ShowColourText'.
      */
-    public boolean getShowColourText()
-    {
+    public boolean getShowColourText(
+    ) {
         return this._showColourText;
-    } //-- boolean getShowColourText() 
+    }
 
     /**
      * Returns the value of field 'showFullId'.
      * 
-     * @return boolean
-     * @return the value of field 'showFullId'.
+     * @return the value of field 'ShowFullId'.
      */
-    public boolean getShowFullId()
-    {
+    public boolean getShowFullId(
+    ) {
         return this._showFullId;
-    } //-- boolean getShowFullId() 
+    }
 
     /**
      * Returns the value of field 'showSequenceFeatures'.
      * 
-     * @return boolean
-     * @return the value of field 'showSequenceFeatures'.
+     * @return the value of field 'ShowSequenceFeatures'.
      */
-    public boolean getShowSequenceFeatures()
-    {
+    public boolean getShowSequenceFeatures(
+    ) {
         return this._showSequenceFeatures;
-    } //-- boolean getShowSequenceFeatures() 
+    }
 
     /**
      * Returns the value of field 'showText'.
      * 
-     * @return boolean
-     * @return the value of field 'showText'.
+     * @return the value of field 'ShowText'.
      */
-    public boolean getShowText()
-    {
+    public boolean getShowText(
+    ) {
         return this._showText;
-    } //-- boolean getShowText() 
+    }
+
+    /**
+     * Returns the value of field 'showUnconserved'.
+     * 
+     * @return the value of field 'ShowUnconserved'.
+     */
+    public boolean getShowUnconserved(
+    ) {
+        return this._showUnconserved;
+    }
 
     /**
      * Returns the value of field 'startRes'.
      * 
-     * @return int
-     * @return the value of field 'startRes'.
+     * @return the value of field 'StartRes'.
      */
-    public int getStartRes()
-    {
+    public int getStartRes(
+    ) {
         return this._startRes;
-    } //-- int getStartRes() 
+    }
 
     /**
      * Returns the value of field 'startSeq'.
      * 
-     * @return int
-     * @return the value of field 'startSeq'.
+     * @return the value of field 'StartSeq'.
      */
-    public int getStartSeq()
-    {
+    public int getStartSeq(
+    ) {
         return this._startSeq;
-    } //-- int getStartSeq() 
+    }
 
     /**
      * Returns the value of field 'textCol1'.
      * 
-     * @return int
-     * @return the value of field 'textCol1'.
+     * @return the value of field 'TextCol1'.
      */
-    public int getTextCol1()
-    {
+    public int getTextCol1(
+    ) {
         return this._textCol1;
-    } //-- int getTextCol1() 
+    }
 
     /**
      * Returns the value of field 'textCol2'.
      * 
-     * @return int
-     * @return the value of field 'textCol2'.
+     * @return the value of field 'TextCol2'.
      */
-    public int getTextCol2()
-    {
+    public int getTextCol2(
+    ) {
         return this._textCol2;
-    } //-- int getTextCol2() 
+    }
 
     /**
      * Returns the value of field 'textColThreshold'.
      * 
-     * @return int
-     * @return the value of field 'textColThreshold'.
+     * @return the value of field 'TextColThreshold'.
      */
-    public int getTextColThreshold()
-    {
+    public int getTextColThreshold(
+    ) {
         return this._textColThreshold;
-    } //-- int getTextColThreshold() 
+    }
 
     /**
      * Returns the value of field 'title'.
      * 
-     * @return String
-     * @return the value of field 'title'.
+     * @return the value of field 'Title'.
      */
-    public java.lang.String getTitle()
-    {
+    public java.lang.String getTitle(
+    ) {
         return this._title;
-    } //-- java.lang.String getTitle() 
+    }
 
     /**
      * Returns the value of field 'viewName'.
      * 
-     * @return String
-     * @return the value of field 'viewName'.
+     * @return the value of field 'ViewName'.
      */
-    public java.lang.String getViewName()
-    {
+    public java.lang.String getViewName(
+    ) {
         return this._viewName;
-    } //-- java.lang.String getViewName() 
+    }
 
     /**
      * Returns the value of field 'width'.
      * 
-     * @return int
-     * @return the value of field 'width'.
+     * @return the value of field 'Width'.
      */
-    public int getWidth()
-    {
+    public int getWidth(
+    ) {
         return this._width;
-    } //-- int getWidth() 
+    }
 
     /**
      * Returns the value of field 'wrapAlignment'.
      * 
-     * @return boolean
-     * @return the value of field 'wrapAlignment'.
+     * @return the value of field 'WrapAlignment'.
      */
-    public boolean getWrapAlignment()
-    {
+    public boolean getWrapAlignment(
+    ) {
         return this._wrapAlignment;
-    } //-- boolean getWrapAlignment() 
+    }
 
     /**
      * Returns the value of field 'xpos'.
      * 
-     * @return int
-     * @return the value of field 'xpos'.
+     * @return the value of field 'Xpos'.
      */
-    public int getXpos()
-    {
+    public int getXpos(
+    ) {
         return this._xpos;
-    } //-- int getXpos() 
+    }
 
     /**
      * Returns the value of field 'ypos'.
      * 
-     * @return int
-     * @return the value of field 'ypos'.
+     * @return the value of field 'Ypos'.
      */
-    public int getYpos()
-    {
+    public int getYpos(
+    ) {
         return this._ypos;
-    } //-- int getYpos() 
+    }
 
     /**
-     * Method hasConsThreshold
+     * Method hasConsThreshold.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one ConsThreshold has been added
      */
-    public boolean hasConsThreshold()
-    {
+    public boolean hasConsThreshold(
+    ) {
         return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
+    }
 
     /**
-     * Method hasConservationSelected
-     * 
+     * Method hasConservationSelected.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one ConservationSelected has been
+     * added
      */
-    public boolean hasConservationSelected()
-    {
+    public boolean hasConservationSelected(
+    ) {
         return this._has_conservationSelected;
-    } //-- boolean hasConservationSelected() 
+    }
 
     /**
-     * Method hasFontSize
-     * 
-     * 
+     * Method hasFontSize.
      * 
-     * @return boolean
+     * @return true if at least one FontSize has been added
      */
-    public boolean hasFontSize()
-    {
+    public boolean hasFontSize(
+    ) {
         return this._has_fontSize;
-    } //-- boolean hasFontSize() 
+    }
 
     /**
-     * Method hasFontStyle
+     * Method hasFontStyle.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one FontStyle has been added
      */
-    public boolean hasFontStyle()
-    {
+    public boolean hasFontStyle(
+    ) {
         return this._has_fontStyle;
-    } //-- boolean hasFontStyle() 
+    }
 
     /**
-     * Method hasGatheredViews
-     * 
+     * Method hasGatheredViews.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one GatheredViews has been added
      */
-    public boolean hasGatheredViews()
-    {
+    public boolean hasGatheredViews(
+    ) {
         return this._has_gatheredViews;
-    } //-- boolean hasGatheredViews() 
+    }
 
     /**
-     * Method hasHeight
-     * 
-     * 
+     * Method hasHeight.
      * 
-     * @return boolean
+     * @return true if at least one Height has been added
      */
-    public boolean hasHeight()
-    {
+    public boolean hasHeight(
+    ) {
         return this._has_height;
-    } //-- boolean hasHeight() 
+    }
 
     /**
-     * Method hasPidSelected
+     * Method hasPidSelected.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one PidSelected has been added
      */
-    public boolean hasPidSelected()
-    {
+    public boolean hasPidSelected(
+    ) {
         return this._has_pidSelected;
-    } //-- boolean hasPidSelected() 
+    }
 
     /**
-     * Method hasPidThreshold
-     * 
+     * Method hasPidThreshold.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one PidThreshold has been added
      */
-    public boolean hasPidThreshold()
-    {
+    public boolean hasPidThreshold(
+    ) {
         return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
+    }
 
     /**
-     * Method hasRenderGaps
-     * 
-     * 
+     * Method hasRenderGaps.
      * 
-     * @return boolean
+     * @return true if at least one RenderGaps has been added
      */
-    public boolean hasRenderGaps()
-    {
+    public boolean hasRenderGaps(
+    ) {
         return this._has_renderGaps;
-    } //-- boolean hasRenderGaps() 
+    }
 
     /**
-     * Method hasRightAlignIds
+     * Method hasRightAlignIds.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one RightAlignIds has been added
      */
-    public boolean hasRightAlignIds()
-    {
+    public boolean hasRightAlignIds(
+    ) {
         return this._has_rightAlignIds;
-    } //-- boolean hasRightAlignIds() 
+    }
 
     /**
-     * Method hasShowAnnotation
-     * 
+     * Method hasShowAnnotation.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowAnnotation has been added
      */
-    public boolean hasShowAnnotation()
-    {
+    public boolean hasShowAnnotation(
+    ) {
         return this._has_showAnnotation;
-    } //-- boolean hasShowAnnotation() 
+    }
 
     /**
-     * Method hasShowBoxes
-     * 
-     * 
+     * Method hasShowBoxes.
      * 
-     * @return boolean
+     * @return true if at least one ShowBoxes has been added
      */
-    public boolean hasShowBoxes()
-    {
+    public boolean hasShowBoxes(
+    ) {
         return this._has_showBoxes;
-    } //-- boolean hasShowBoxes() 
+    }
 
     /**
-     * Method hasShowColourText
+     * Method hasShowColourText.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowColourText has been added
      */
-    public boolean hasShowColourText()
-    {
+    public boolean hasShowColourText(
+    ) {
         return this._has_showColourText;
-    } //-- boolean hasShowColourText() 
+    }
 
     /**
-     * Method hasShowFullId
-     * 
+     * Method hasShowFullId.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowFullId has been added
      */
-    public boolean hasShowFullId()
-    {
+    public boolean hasShowFullId(
+    ) {
         return this._has_showFullId;
-    } //-- boolean hasShowFullId() 
+    }
 
     /**
-     * Method hasShowSequenceFeatures
-     * 
-     * 
+     * Method hasShowSequenceFeatures.
      * 
-     * @return boolean
+     * @return true if at least one ShowSequenceFeatures has been
+     * added
      */
-    public boolean hasShowSequenceFeatures()
-    {
+    public boolean hasShowSequenceFeatures(
+    ) {
         return this._has_showSequenceFeatures;
-    } //-- boolean hasShowSequenceFeatures() 
+    }
 
     /**
-     * Method hasShowText
+     * Method hasShowText.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one ShowText has been added
      */
-    public boolean hasShowText()
-    {
+    public boolean hasShowText(
+    ) {
         return this._has_showText;
-    } //-- boolean hasShowText() 
+    }
 
     /**
-     * Method hasStartRes
-     * 
+     * Method hasShowUnconserved.
      * 
+     * @return true if at least one ShowUnconserved has been added
+     */
+    public boolean hasShowUnconserved(
+    ) {
+        return this._has_showUnconserved;
+    }
+
+    /**
+     * Method hasStartRes.
      * 
-     * @return boolean
+     * @return true if at least one StartRes has been added
      */
-    public boolean hasStartRes()
-    {
+    public boolean hasStartRes(
+    ) {
         return this._has_startRes;
-    } //-- boolean hasStartRes() 
+    }
 
     /**
-     * Method hasStartSeq
+     * Method hasStartSeq.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one StartSeq has been added
      */
-    public boolean hasStartSeq()
-    {
+    public boolean hasStartSeq(
+    ) {
         return this._has_startSeq;
-    } //-- boolean hasStartSeq() 
+    }
 
     /**
-     * Method hasTextCol1
-     * 
+     * Method hasTextCol1.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one TextCol1 has been added
      */
-    public boolean hasTextCol1()
-    {
+    public boolean hasTextCol1(
+    ) {
         return this._has_textCol1;
-    } //-- boolean hasTextCol1() 
+    }
 
     /**
-     * Method hasTextCol2
-     * 
-     * 
+     * Method hasTextCol2.
      * 
-     * @return boolean
+     * @return true if at least one TextCol2 has been added
      */
-    public boolean hasTextCol2()
-    {
+    public boolean hasTextCol2(
+    ) {
         return this._has_textCol2;
-    } //-- boolean hasTextCol2() 
+    }
 
     /**
-     * Method hasTextColThreshold
+     * Method hasTextColThreshold.
      * 
+     * @return true if at least one TextColThreshold has been added
+     */
+    public boolean hasTextColThreshold(
+    ) {
+        return this._has_textColThreshold;
+    }
+
+    /**
+     * Method hasWidth.
      * 
+     * @return true if at least one Width has been added
+     */
+    public boolean hasWidth(
+    ) {
+        return this._has_width;
+    }
+
+    /**
+     * Method hasWrapAlignment.
      * 
-     * @return boolean
+     * @return true if at least one WrapAlignment has been added
      */
-    public boolean hasTextColThreshold()
-    {
-        return this._has_textColThreshold;
-    } //-- boolean hasTextColThreshold() 
+    public boolean hasWrapAlignment(
+    ) {
+        return this._has_wrapAlignment;
+    }
 
     /**
-     * Method hasWidth
+     * Method hasXpos.
      * 
+     * @return true if at least one Xpos has been added
+     */
+    public boolean hasXpos(
+    ) {
+        return this._has_xpos;
+    }
+
+    /**
+     * Method hasYpos.
      * 
+     * @return true if at least one Ypos has been added
+     */
+    public boolean hasYpos(
+    ) {
+        return this._has_ypos;
+    }
+
+    /**
+     * Returns the value of field 'conservationSelected'.
      * 
-     * @return boolean
+     * @return the value of field 'ConservationSelected'.
      */
-    public boolean hasWidth()
-    {
-        return this._has_width;
-    } //-- boolean hasWidth() 
+    public boolean isConservationSelected(
+    ) {
+        return this._conservationSelected;
+    }
 
     /**
-     * Method hasWrapAlignment
+     * Returns the value of field 'gatheredViews'.
      * 
+     * @return the value of field 'GatheredViews'.
+     */
+    public boolean isGatheredViews(
+    ) {
+        return this._gatheredViews;
+    }
+
+    /**
+     * Returns the value of field 'pidSelected'.
      * 
+     * @return the value of field 'PidSelected'.
+     */
+    public boolean isPidSelected(
+    ) {
+        return this._pidSelected;
+    }
+
+    /**
+     * Returns the value of field 'renderGaps'.
      * 
-     * @return boolean
+     * @return the value of field 'RenderGaps'.
      */
-    public boolean hasWrapAlignment()
-    {
-        return this._has_wrapAlignment;
-    } //-- boolean hasWrapAlignment() 
+    public boolean isRenderGaps(
+    ) {
+        return this._renderGaps;
+    }
 
     /**
-     * Method hasXpos
+     * Returns the value of field 'rightAlignIds'.
      * 
+     * @return the value of field 'RightAlignIds'.
+     */
+    public boolean isRightAlignIds(
+    ) {
+        return this._rightAlignIds;
+    }
+
+    /**
+     * Returns the value of field 'showAnnotation'.
      * 
+     * @return the value of field 'ShowAnnotation'.
+     */
+    public boolean isShowAnnotation(
+    ) {
+        return this._showAnnotation;
+    }
+
+    /**
+     * Returns the value of field 'showBoxes'.
      * 
-     * @return boolean
+     * @return the value of field 'ShowBoxes'.
      */
-    public boolean hasXpos()
-    {
-        return this._has_xpos;
-    } //-- boolean hasXpos() 
+    public boolean isShowBoxes(
+    ) {
+        return this._showBoxes;
+    }
 
     /**
-     * Method hasYpos
+     * Returns the value of field 'showColourText'.
      * 
+     * @return the value of field 'ShowColourText'.
+     */
+    public boolean isShowColourText(
+    ) {
+        return this._showColourText;
+    }
+
+    /**
+     * Returns the value of field 'showFullId'.
      * 
+     * @return the value of field 'ShowFullId'.
+     */
+    public boolean isShowFullId(
+    ) {
+        return this._showFullId;
+    }
+
+    /**
+     * Returns the value of field 'showSequenceFeatures'.
      * 
-     * @return boolean
+     * @return the value of field 'ShowSequenceFeatures'.
      */
-    public boolean hasYpos()
-    {
-        return this._has_ypos;
-    } //-- boolean hasYpos() 
+    public boolean isShowSequenceFeatures(
+    ) {
+        return this._showSequenceFeatures;
+    }
 
     /**
-     * Method isValid
+     * Returns the value of field 'showText'.
      * 
+     * @return the value of field 'ShowText'.
+     */
+    public boolean isShowText(
+    ) {
+        return this._showText;
+    }
+
+    /**
+     * Returns the value of field 'showUnconserved'.
      * 
+     * @return the value of field 'ShowUnconserved'.
+     */
+    public boolean isShowUnconserved(
+    ) {
+        return this._showUnconserved;
+    }
+
+    /**
+     * Method isValid.
      * 
-     * @return boolean
+     * @return true if this object is valid according to the schema
      */
-    public boolean isValid()
-    {
+    public boolean isValid(
+    ) {
         try {
             validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        } catch (org.exolab.castor.xml.ValidationException vex) {
             return false;
         }
         return true;
-    } //-- boolean isValid() 
+    }
 
     /**
-     * Method marshal
+     * Returns the value of field 'wrapAlignment'.
      * 
+     * @return the value of field 'WrapAlignment'.
+     */
+    public boolean isWrapAlignment(
+    ) {
+        return this._wrapAlignment;
+    }
+
+    /**
      * 
      * 
      * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    }
 
     /**
-     * Method marshal
-     * 
      * 
      * 
      * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    }
 
     /**
-     * Method removeAllHiddenColumns
-     * 
      */
-    public void removeAllHiddenColumns()
-    {
-        _hiddenColumnsList.removeAllElements();
-    } //-- void removeAllHiddenColumns() 
+    public void removeAllHiddenColumns(
+    ) {
+        this._hiddenColumnsList.clear();
+    }
 
     /**
-     * Method removeHiddenColumns
-     * 
+     * Method removeHiddenColumns.
      * 
+     * @param vHiddenColumns
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeHiddenColumns(
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
+        boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+        return removed;
+    }
+
+    /**
+     * Method removeHiddenColumnsAt.
      * 
      * @param index
-     * @return HiddenColumns
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)
-    {
-        java.lang.Object obj = _hiddenColumnsList.elementAt(index);
-        _hiddenColumnsList.removeElementAt(index);
+    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+            final int index) {
+        java.lang.Object obj = this._hiddenColumnsList.remove(index);
         return (jalview.schemabinding.version2.HiddenColumns) obj;
-    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) 
+    }
 
     /**
      * Sets the value of field 'annotationColours'.
@@ -1364,31 +1420,31 @@ public class Viewport implements java.io.Serializable {
      * @param annotationColours the value of field
      * 'annotationColours'.
      */
-    public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)
-    {
+    public void setAnnotationColours(
+            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
         this._annotationColours = annotationColours;
-    } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) 
+    }
 
     /**
      * Sets the value of field 'bgColour'.
      * 
      * @param bgColour the value of field 'bgColour'.
      */
-    public void setBgColour(java.lang.String bgColour)
-    {
+    public void setBgColour(
+            final 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)
-    {
+    public void setConsThreshold(
+            final int consThreshold) {
         this._consThreshold = consThreshold;
         this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
+    }
 
     /**
      * Sets the value of field 'conservationSelected'.
@@ -1396,197 +1452,211 @@ public class Viewport implements java.io.Serializable {
      * @param conservationSelected the value of field
      * 'conservationSelected'.
      */
-    public void setConservationSelected(boolean conservationSelected)
-    {
+    public void setConservationSelected(
+            final 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)
-    {
+    public void setFontName(
+            final 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)
-    {
+    public void setFontSize(
+            final 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)
-    {
+    public void setFontStyle(
+            final int fontStyle) {
         this._fontStyle = fontStyle;
         this._has_fontStyle = true;
-    } //-- void setFontStyle(int) 
+    }
 
     /**
      * Sets the value of field 'gatheredViews'.
      * 
      * @param gatheredViews the value of field 'gatheredViews'.
      */
-    public void setGatheredViews(boolean gatheredViews)
-    {
+    public void setGatheredViews(
+            final boolean gatheredViews) {
         this._gatheredViews = gatheredViews;
         this._has_gatheredViews = true;
-    } //-- void setGatheredViews(boolean) 
+    }
 
     /**
      * Sets the value of field 'height'.
      * 
      * @param height the value of field 'height'.
      */
-    public void setHeight(int height)
-    {
+    public void setHeight(
+            final int height) {
         this._height = height;
         this._has_height = true;
-    } //-- void setHeight(int) 
+    }
 
     /**
-     * Method setHiddenColumns
-     * 
      * 
      * 
      * @param index
      * @param vHiddenColumns
-     */
-    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setHiddenColumns(
+            final int index,
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenColumnsList.size()) {
+            throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
         }
-        _hiddenColumnsList.setElementAt(vHiddenColumns, index);
-    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
+        
+        this._hiddenColumnsList.set(index, vHiddenColumns);
+    }
 
     /**
-     * Method setHiddenColumns
-     * 
      * 
      * 
-     * @param hiddenColumnsArray
+     * @param vHiddenColumnsArray
      */
-    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)
-    {
+    public void setHiddenColumns(
+            final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
         //-- copy array
-        _hiddenColumnsList.removeAllElements();
-        for (int i = 0; i < hiddenColumnsArray.length; i++) {
-            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
+        _hiddenColumnsList.clear();
+        
+        for (int i = 0; i < vHiddenColumnsArray.length; i++) {
+                this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
         }
-    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
+    }
+
+    /**
+     * Sets the value of field 'id'. The field 'id' has the
+     * following description: unique id used by jalview to
+     * synchronize between stored and instantiated views
+     *  
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(
+            final java.lang.String id) {
+        this._id = id;
+    }
 
     /**
      * Sets the value of field 'pidSelected'.
      * 
      * @param pidSelected the value of field 'pidSelected'.
      */
-    public void setPidSelected(boolean pidSelected)
-    {
+    public void setPidSelected(
+            final 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)
-    {
+    public void setPidThreshold(
+            final 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)
-    {
+    public void setRenderGaps(
+            final boolean renderGaps) {
         this._renderGaps = renderGaps;
         this._has_renderGaps = true;
-    } //-- void setRenderGaps(boolean) 
+    }
 
     /**
      * Sets the value of field 'rightAlignIds'.
      * 
      * @param rightAlignIds the value of field 'rightAlignIds'.
      */
-    public void setRightAlignIds(boolean rightAlignIds)
-    {
+    public void setRightAlignIds(
+            final boolean rightAlignIds) {
         this._rightAlignIds = rightAlignIds;
         this._has_rightAlignIds = true;
-    } //-- void setRightAlignIds(boolean) 
+    }
 
     /**
      * Sets the value of field 'sequenceSetId'.
      * 
      * @param sequenceSetId the value of field 'sequenceSetId'.
      */
-    public void setSequenceSetId(java.lang.String sequenceSetId)
-    {
+    public void setSequenceSetId(
+            final java.lang.String sequenceSetId) {
         this._sequenceSetId = sequenceSetId;
-    } //-- void setSequenceSetId(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'showAnnotation'.
      * 
      * @param showAnnotation the value of field 'showAnnotation'.
      */
-    public void setShowAnnotation(boolean showAnnotation)
-    {
+    public void setShowAnnotation(
+            final 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)
-    {
+    public void setShowBoxes(
+            final 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)
-    {
+    public void setShowColourText(
+            final boolean showColourText) {
         this._showColourText = showColourText;
         this._has_showColourText = true;
-    } //-- void setShowColourText(boolean) 
+    }
 
     /**
      * Sets the value of field 'showFullId'.
      * 
      * @param showFullId the value of field 'showFullId'.
      */
-    public void setShowFullId(boolean showFullId)
-    {
+    public void setShowFullId(
+            final boolean showFullId) {
         this._showFullId = showFullId;
         this._has_showFullId = true;
-    } //-- void setShowFullId(boolean) 
+    }
 
     /**
      * Sets the value of field 'showSequenceFeatures'.
@@ -1594,165 +1664,181 @@ public class Viewport implements java.io.Serializable {
      * @param showSequenceFeatures the value of field
      * 'showSequenceFeatures'.
      */
-    public void setShowSequenceFeatures(boolean showSequenceFeatures)
-    {
+    public void setShowSequenceFeatures(
+            final 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)
-    {
+    public void setShowText(
+            final boolean showText) {
         this._showText = showText;
         this._has_showText = true;
-    } //-- void setShowText(boolean) 
+    }
+
+    /**
+     * Sets the value of field 'showUnconserved'.
+     * 
+     * @param showUnconserved the value of field 'showUnconserved'.
+     */
+    public void setShowUnconserved(
+            final boolean showUnconserved) {
+        this._showUnconserved = showUnconserved;
+        this._has_showUnconserved = true;
+    }
 
     /**
      * Sets the value of field 'startRes'.
      * 
      * @param startRes the value of field 'startRes'.
      */
-    public void setStartRes(int startRes)
-    {
+    public void setStartRes(
+            final 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)
-    {
+    public void setStartSeq(
+            final int startSeq) {
         this._startSeq = startSeq;
         this._has_startSeq = true;
-    } //-- void setStartSeq(int) 
+    }
 
     /**
      * Sets the value of field 'textCol1'.
      * 
      * @param textCol1 the value of field 'textCol1'.
      */
-    public void setTextCol1(int textCol1)
-    {
+    public void setTextCol1(
+            final 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)
-    {
+    public void setTextCol2(
+            final 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)
-    {
+    public void setTextColThreshold(
+            final int textColThreshold) {
         this._textColThreshold = textColThreshold;
         this._has_textColThreshold = true;
-    } //-- void setTextColThreshold(int) 
+    }
 
     /**
      * Sets the value of field 'title'.
      * 
      * @param title the value of field 'title'.
      */
-    public void setTitle(java.lang.String title)
-    {
+    public void setTitle(
+            final java.lang.String title) {
         this._title = title;
-    } //-- void setTitle(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'viewName'.
      * 
      * @param viewName the value of field 'viewName'.
      */
-    public void setViewName(java.lang.String viewName)
-    {
+    public void setViewName(
+            final java.lang.String viewName) {
         this._viewName = viewName;
-    } //-- void setViewName(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'width'.
      * 
      * @param width the value of field 'width'.
      */
-    public void setWidth(int width)
-    {
+    public void setWidth(
+            final 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)
-    {
+    public void setWrapAlignment(
+            final 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)
-    {
+    public void setXpos(
+            final 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)
-    {
+    public void setYpos(
+            final int ypos) {
         this._ypos = ypos;
         this._has_ypos = true;
-    } //-- void setYpos(int) 
+    }
 
     /**
-     * Method unmarshal
-     * 
-     * 
+     * Method unmarshal.
      * 
      * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled
+     * jalview.schemabinding.version2.Viewport
+     */
+    public static jalview.schemabinding.version2.Viewport unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+    }
 
     /**
-     * Method validate
      * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
 }