fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view...

[jalview.git] / src / jalview / schemabinding / version2 / Viewport.java

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 24adba5..49b0db2 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,6 +1,6 @@
 /*\r
  * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
  * Schema.\r
  * $Id$\r
  */\r
@@ -11,17 +11,8 @@ package jalview.schemabinding.version2;
  //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
 import org.exolab.castor.xml.Marshaller;\r
 import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Viewport.\r
@@ -36,7 +27,7 @@ public class Viewport implements java.io.Serializable {
     //--------------------------/\r
 \r
     /**\r
-     * Field _conservationSelected\r
+     * Field _conservationSelected.\r
      */\r
     private boolean _conservationSelected;\r
 \r
@@ -46,7 +37,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_conservationSelected;\r
 \r
     /**\r
-     * Field _pidSelected\r
+     * Field _pidSelected.\r
      */\r
     private boolean _pidSelected;\r
 \r
@@ -56,12 +47,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_pidSelected;\r
 \r
     /**\r
-     * Field _bgColour\r
+     * Field _bgColour.\r
      */\r
     private java.lang.String _bgColour;\r
 \r
     /**\r
-     * Field _consThreshold\r
+     * Field _consThreshold.\r
      */\r
     private int _consThreshold;\r
 \r
@@ -71,7 +62,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_consThreshold;\r
 \r
     /**\r
-     * Field _pidThreshold\r
+     * Field _pidThreshold.\r
      */\r
     private int _pidThreshold;\r
 \r
@@ -81,12 +72,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_pidThreshold;\r
 \r
     /**\r
-     * Field _title\r
+     * Field _title.\r
      */\r
     private java.lang.String _title;\r
 \r
     /**\r
-     * Field _showFullId\r
+     * Field _showFullId.\r
      */\r
     private boolean _showFullId;\r
 \r
@@ -96,7 +87,17 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showFullId;\r
 \r
     /**\r
-     * Field _showText\r
+     * Field _rightAlignIds.\r
+     */\r
+    private boolean _rightAlignIds;\r
+\r
+    /**\r
+     * keeps track of state for field: _rightAlignIds\r
+     */\r
+    private boolean _has_rightAlignIds;\r
+\r
+    /**\r
+     * Field _showText.\r
      */\r
     private boolean _showText;\r
 \r
@@ -106,7 +107,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showText;\r
 \r
     /**\r
-     * Field _showColourText\r
+     * Field _showColourText.\r
      */\r
     private boolean _showColourText;\r
 \r
@@ -116,7 +117,17 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showColourText;\r
 \r
     /**\r
-     * Field _showBoxes\r
+     * Field _showUnconserved.\r
+     */\r
+    private boolean _showUnconserved = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showUnconserved\r
+     */\r
+    private boolean _has_showUnconserved;\r
+\r
+    /**\r
+     * Field _showBoxes.\r
      */\r
     private boolean _showBoxes;\r
 \r
@@ -126,7 +137,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showBoxes;\r
 \r
     /**\r
-     * Field _wrapAlignment\r
+     * Field _wrapAlignment.\r
      */\r
     private boolean _wrapAlignment;\r
 \r
@@ -136,7 +147,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_wrapAlignment;\r
 \r
     /**\r
-     * Field _renderGaps\r
+     * Field _renderGaps.\r
      */\r
     private boolean _renderGaps;\r
 \r
@@ -146,7 +157,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_renderGaps;\r
 \r
     /**\r
-     * Field _showSequenceFeatures\r
+     * Field _showSequenceFeatures.\r
      */\r
     private boolean _showSequenceFeatures;\r
 \r
@@ -156,7 +167,47 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showSequenceFeatures;\r
 \r
     /**\r
-     * Field _showAnnotation\r
+     * Field _showNPfeatureTooltip.\r
+     */\r
+    private boolean _showNPfeatureTooltip;\r
+\r
+    /**\r
+     * keeps track of state for field: _showNPfeatureTooltip\r
+     */\r
+    private boolean _has_showNPfeatureTooltip;\r
+\r
+    /**\r
+     * Field _showDbRefTooltip.\r
+     */\r
+    private boolean _showDbRefTooltip;\r
+\r
+    /**\r
+     * keeps track of state for field: _showDbRefTooltip\r
+     */\r
+    private boolean _has_showDbRefTooltip;\r
+\r
+    /**\r
+     * Field _followHighlight.\r
+     */\r
+    private boolean _followHighlight = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _followHighlight\r
+     */\r
+    private boolean _has_followHighlight;\r
+\r
+    /**\r
+     * Field _followSelection.\r
+     */\r
+    private boolean _followSelection = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _followSelection\r
+     */\r
+    private boolean _has_followSelection;\r
+\r
+    /**\r
+     * Field _showAnnotation.\r
      */\r
     private boolean _showAnnotation;\r
 \r
@@ -166,37 +217,67 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showAnnotation;\r
 \r
     /**\r
-     * Field _showConservation\r
+     * Field _centreColumnLabels.\r
+     */\r
+    private boolean _centreColumnLabels = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _centreColumnLabels\r
+     */\r
+    private boolean _has_centreColumnLabels;\r
+\r
+    /**\r
+     * Field _showGroupConservation.\r
+     */\r
+    private boolean _showGroupConservation = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showGroupConservation\r
+     */\r
+    private boolean _has_showGroupConservation;\r
+\r
+    /**\r
+     * Field _showGroupConsensus.\r
+     */\r
+    private boolean _showGroupConsensus = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showGroupConsensus\r
+     */\r
+    private boolean _has_showGroupConsensus;\r
+\r
+    /**\r
+     * Field _showConsensusHistogram.\r
      */\r
-    private boolean _showConservation;\r
+    private boolean _showConsensusHistogram = true;\r
 \r
     /**\r
-     * keeps track of state for field: _showConservation\r
+     * keeps track of state for field: _showConsensusHistogram\r
      */\r
-    private boolean _has_showConservation;\r
+    private boolean _has_showConsensusHistogram;\r
 \r
     /**\r
-     * Field _showQuality\r
+     * Field _showSequenceLogo.\r
      */\r
-    private boolean _showQuality;\r
+    private boolean _showSequenceLogo = false;\r
 \r
     /**\r
-     * keeps track of state for field: _showQuality\r
+     * keeps track of state for field: _showSequenceLogo\r
      */\r
-    private boolean _has_showQuality;\r
+    private boolean _has_showSequenceLogo;\r
 \r
     /**\r
-     * Field _showIdentity\r
+     * Field _ignoreGapsinConsensus.\r
      */\r
-    private boolean _showIdentity;\r
+    private boolean _ignoreGapsinConsensus = true;\r
 \r
     /**\r
-     * keeps track of state for field: _showIdentity\r
+     * keeps track of state for field: _ignoreGapsinConsensus\r
      */\r
-    private boolean _has_showIdentity;\r
+    private boolean _has_ignoreGapsinConsensus;\r
 \r
     /**\r
-     * Field _xpos\r
+     * Field _xpos.\r
      */\r
     private int _xpos;\r
 \r
@@ -206,7 +287,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_xpos;\r
 \r
     /**\r
-     * Field _ypos\r
+     * Field _ypos.\r
      */\r
     private int _ypos;\r
 \r
@@ -216,7 +297,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_ypos;\r
 \r
     /**\r
-     * Field _width\r
+     * Field _width.\r
      */\r
     private int _width;\r
 \r
@@ -226,7 +307,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_width;\r
 \r
     /**\r
-     * Field _height\r
+     * Field _height.\r
      */\r
     private int _height;\r
 \r
@@ -236,7 +317,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_height;\r
 \r
     /**\r
-     * Field _startRes\r
+     * Field _startRes.\r
      */\r
     private int _startRes;\r
 \r
@@ -246,7 +327,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_startRes;\r
 \r
     /**\r
-     * Field _startSeq\r
+     * Field _startSeq.\r
      */\r
     private int _startSeq;\r
 \r
@@ -256,12 +337,12 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_startSeq;\r
 \r
     /**\r
-     * Field _fontName\r
+     * Field _fontName.\r
      */\r
     private java.lang.String _fontName;\r
 \r
     /**\r
-     * Field _fontSize\r
+     * Field _fontSize.\r
      */\r
     private int _fontSize;\r
 \r
@@ -271,7 +352,7 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontSize;\r
 \r
     /**\r
-     * Field _fontStyle\r
+     * Field _fontStyle.\r
      */\r
     private int _fontStyle;\r
 \r
@@ -281,17 +362,17 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontStyle;\r
 \r
     /**\r
-     * Field _viewName\r
+     * Field _viewName.\r
      */\r
     private java.lang.String _viewName;\r
 \r
     /**\r
-     * Field _sequenceSetId\r
+     * Field _sequenceSetId.\r
      */\r
     private java.lang.String _sequenceSetId;\r
 \r
     /**\r
-     * Field _gatheredViews\r
+     * Field _gatheredViews.\r
      */\r
     private boolean _gatheredViews;\r
 \r
@@ -301,12 +382,49 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_gatheredViews;\r
 \r
     /**\r
-     * Field _annotationColours\r
+     * Field _textCol1.\r
+     */\r
+    private int _textCol1;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol1\r
+     */\r
+    private boolean _has_textCol1;\r
+\r
+    /**\r
+     * Field _textCol2.\r
+     */\r
+    private int _textCol2;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol2\r
+     */\r
+    private boolean _has_textCol2;\r
+\r
+    /**\r
+     * Field _textColThreshold.\r
+     */\r
+    private int _textColThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _textColThreshold\r
+     */\r
+    private boolean _has_textColThreshold;\r
+\r
+    /**\r
+     * unique id used by jalview to synchronize between stored and\r
+     * instantiated views\r
+     *  \r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _annotationColours.\r
      */\r
     private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
 \r
     /**\r
-     * Field _hiddenColumnsList\r
+     * Field _hiddenColumnsList.\r
      */\r
     private java.util.Vector _hiddenColumnsList;\r
 \r
@@ -317,8 +435,8 @@ public class Viewport implements java.io.Serializable {
 \r
     public Viewport() {\r
         super();\r
-        _hiddenColumnsList = new Vector();\r
-    } //-- jalview.schemabinding.version2.Viewport()\r
+        this._hiddenColumnsList = new java.util.Vector();\r
+    }\r
 \r
 \r
       //-----------/\r
@@ -326,995 +444,1449 @@ public class Viewport implements java.io.Serializable {
     //-----------/\r
 \r
     /**\r
-     * Method addHiddenColumns\r
-     * \r
      * \r
      * \r
      * @param vHiddenColumns\r
+     * @throws java.lang.IndexOutOfBoundsException if the index\r
+     * given is outside the bounds of the collection\r
      */\r
-    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        _hiddenColumnsList.addElement(vHiddenColumns);\r
-    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+    public void addHiddenColumns(\r
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+    throws java.lang.IndexOutOfBoundsException {\r
+        this._hiddenColumnsList.addElement(vHiddenColumns);\r
+    }\r
 \r
     /**\r
-     * Method addHiddenColumns\r
-     * \r
      * \r
      * \r
      * @param index\r
      * @param vHiddenColumns\r
+     * @throws java.lang.IndexOutOfBoundsException if the index\r
+     * given is outside the bounds of the collection\r
      */\r
-    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
-    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+    public void addHiddenColumns(\r
+            final int index,\r
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+    throws java.lang.IndexOutOfBoundsException {\r
+        this._hiddenColumnsList.add(index, vHiddenColumns);\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteCentreColumnLabels(\r
+    ) {\r
+        this._has_centreColumnLabels= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteConsThreshold\r
-     * \r
      */\r
-    public void deleteConsThreshold()\r
-    {\r
+    public void deleteConsThreshold(\r
+    ) {\r
         this._has_consThreshold= false;\r
-    } //-- void deleteConsThreshold() \r
+    }\r
 \r
     /**\r
-     * Method deleteConservationSelected\r
-     * \r
      */\r
-    public void deleteConservationSelected()\r
-    {\r
+    public void deleteConservationSelected(\r
+    ) {\r
         this._has_conservationSelected= false;\r
-    } //-- void deleteConservationSelected() \r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteFollowHighlight(\r
+    ) {\r
+        this._has_followHighlight= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteFollowSelection(\r
+    ) {\r
+        this._has_followSelection= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteFontSize\r
-     * \r
      */\r
-    public void deleteFontSize()\r
-    {\r
+    public void deleteFontSize(\r
+    ) {\r
         this._has_fontSize= false;\r
-    } //-- void deleteFontSize() \r
+    }\r
 \r
     /**\r
-     * Method deleteFontStyle\r
-     * \r
      */\r
-    public void deleteFontStyle()\r
-    {\r
+    public void deleteFontStyle(\r
+    ) {\r
         this._has_fontStyle= false;\r
-    } //-- void deleteFontStyle() \r
+    }\r
 \r
     /**\r
-     * Method deleteGatheredViews\r
-     * \r
      */\r
-    public void deleteGatheredViews()\r
-    {\r
+    public void deleteGatheredViews(\r
+    ) {\r
         this._has_gatheredViews= false;\r
-    } //-- void deleteGatheredViews() \r
+    }\r
 \r
     /**\r
-     * Method deleteHeight\r
-     * \r
      */\r
-    public void deleteHeight()\r
-    {\r
+    public void deleteHeight(\r
+    ) {\r
         this._has_height= false;\r
-    } //-- void deleteHeight() \r
+    }\r
 \r
     /**\r
-     * Method deletePidSelected\r
-     * \r
      */\r
-    public void deletePidSelected()\r
-    {\r
+    public void deleteIgnoreGapsinConsensus(\r
+    ) {\r
+        this._has_ignoreGapsinConsensus= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deletePidSelected(\r
+    ) {\r
         this._has_pidSelected= false;\r
-    } //-- void deletePidSelected() \r
+    }\r
 \r
     /**\r
-     * Method deletePidThreshold\r
-     * \r
      */\r
-    public void deletePidThreshold()\r
-    {\r
+    public void deletePidThreshold(\r
+    ) {\r
         this._has_pidThreshold= false;\r
-    } //-- void deletePidThreshold() \r
+    }\r
 \r
     /**\r
-     * Method deleteRenderGaps\r
-     * \r
      */\r
-    public void deleteRenderGaps()\r
-    {\r
+    public void deleteRenderGaps(\r
+    ) {\r
         this._has_renderGaps= false;\r
-    } //-- void deleteRenderGaps() \r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteRightAlignIds(\r
+    ) {\r
+        this._has_rightAlignIds= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteShowAnnotation\r
-     * \r
      */\r
-    public void deleteShowAnnotation()\r
-    {\r
+    public void deleteShowAnnotation(\r
+    ) {\r
         this._has_showAnnotation= false;\r
-    } //-- void deleteShowAnnotation() \r
+    }\r
 \r
     /**\r
-     * Method deleteShowBoxes\r
-     * \r
      */\r
-    public void deleteShowBoxes()\r
-    {\r
+    public void deleteShowBoxes(\r
+    ) {\r
         this._has_showBoxes= false;\r
-    } //-- void deleteShowBoxes() \r
+    }\r
 \r
     /**\r
-     * Method deleteShowColourText\r
-     * \r
      */\r
-    public void deleteShowColourText()\r
-    {\r
+    public void deleteShowColourText(\r
+    ) {\r
         this._has_showColourText= false;\r
-    } //-- void deleteShowColourText() \r
+    }\r
 \r
     /**\r
-     * Method deleteShowConservation\r
-     * \r
      */\r
-    public void deleteShowConservation()\r
-    {\r
-        this._has_showConservation= false;\r
-    } //-- void deleteShowConservation() \r
+    public void deleteShowConsensusHistogram(\r
+    ) {\r
+        this._has_showConsensusHistogram= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowDbRefTooltip(\r
+    ) {\r
+        this._has_showDbRefTooltip= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteShowFullId\r
-     * \r
      */\r
-    public void deleteShowFullId()\r
-    {\r
+    public void deleteShowFullId(\r
+    ) {\r
         this._has_showFullId= false;\r
-    } //-- void deleteShowFullId() \r
+    }\r
 \r
     /**\r
-     * Method deleteShowIdentity\r
-     * \r
      */\r
-    public void deleteShowIdentity()\r
-    {\r
-        this._has_showIdentity= false;\r
-    } //-- void deleteShowIdentity() \r
+    public void deleteShowGroupConsensus(\r
+    ) {\r
+        this._has_showGroupConsensus= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteShowQuality\r
-     * \r
      */\r
-    public void deleteShowQuality()\r
-    {\r
-        this._has_showQuality= false;\r
-    } //-- void deleteShowQuality() \r
+    public void deleteShowGroupConservation(\r
+    ) {\r
+        this._has_showGroupConservation= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowNPfeatureTooltip(\r
+    ) {\r
+        this._has_showNPfeatureTooltip= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteShowSequenceFeatures\r
-     * \r
      */\r
-    public void deleteShowSequenceFeatures()\r
-    {\r
+    public void deleteShowSequenceFeatures(\r
+    ) {\r
         this._has_showSequenceFeatures= false;\r
-    } //-- void deleteShowSequenceFeatures() \r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowSequenceLogo(\r
+    ) {\r
+        this._has_showSequenceLogo= false;\r
+    }\r
 \r
     /**\r
-     * Method deleteShowText\r
-     * \r
      */\r
-    public void deleteShowText()\r
-    {\r
+    public void deleteShowText(\r
+    ) {\r
         this._has_showText= false;\r
-    } //-- void deleteShowText() \r
+    }\r
 \r
     /**\r
-     * Method deleteStartRes\r
-     * \r
      */\r
-    public void deleteStartRes()\r
-    {\r
+    public void deleteShowUnconserved(\r
+    ) {\r
+        this._has_showUnconserved= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteStartRes(\r
+    ) {\r
         this._has_startRes= false;\r
-    } //-- void deleteStartRes() \r
+    }\r
 \r
     /**\r
-     * Method deleteStartSeq\r
-     * \r
      */\r
-    public void deleteStartSeq()\r
-    {\r
+    public void deleteStartSeq(\r
+    ) {\r
         this._has_startSeq= false;\r
-    } //-- void deleteStartSeq() \r
+    }\r
 \r
     /**\r
-     * Method deleteWidth\r
-     * \r
      */\r
-    public void deleteWidth()\r
-    {\r
+    public void deleteTextCol1(\r
+    ) {\r
+        this._has_textCol1= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteTextCol2(\r
+    ) {\r
+        this._has_textCol2= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteTextColThreshold(\r
+    ) {\r
+        this._has_textColThreshold= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteWidth(\r
+    ) {\r
         this._has_width= false;\r
-    } //-- void deleteWidth() \r
+    }\r
 \r
     /**\r
-     * Method deleteWrapAlignment\r
-     * \r
      */\r
-    public void deleteWrapAlignment()\r
-    {\r
+    public void deleteWrapAlignment(\r
+    ) {\r
         this._has_wrapAlignment= false;\r
-    } //-- void deleteWrapAlignment() \r
+    }\r
 \r
     /**\r
-     * Method deleteXpos\r
-     * \r
      */\r
-    public void deleteXpos()\r
-    {\r
+    public void deleteXpos(\r
+    ) {\r
         this._has_xpos= false;\r
-    } //-- void deleteXpos() \r
+    }\r
 \r
     /**\r
-     * Method deleteYpos\r
-     * \r
      */\r
-    public void deleteYpos()\r
-    {\r
+    public void deleteYpos(\r
+    ) {\r
         this._has_ypos= false;\r
-    } //-- void deleteYpos() \r
+    }\r
 \r
     /**\r
-     * Method enumerateHiddenColumns\r
-     * \r
-     * \r
+     * Method enumerateHiddenColumns.\r
      * \r
-     * @return Enumeration\r
+     * @return an Enumeration over all\r
+     * jalview.schemabinding.version2.HiddenColumns elements\r
      */\r
-    public java.util.Enumeration enumerateHiddenColumns()\r
-    {\r
-        return _hiddenColumnsList.elements();\r
-    } //-- java.util.Enumeration enumerateHiddenColumns() \r
+    public java.util.Enumeration enumerateHiddenColumns(\r
+    ) {\r
+        return this._hiddenColumnsList.elements();\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'annotationColours'.\r
      * \r
-     * @return AnnotationColours\r
-     * @return the value of field 'annotationColours'.\r
+     * @return the value of field 'AnnotationColours'.\r
      */\r
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
-    {\r
+    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(\r
+    ) {\r
         return this._annotationColours;\r
-    } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'bgColour'.\r
      * \r
-     * @return String\r
-     * @return the value of field 'bgColour'.\r
+     * @return the value of field 'BgColour'.\r
      */\r
-    public java.lang.String getBgColour()\r
-    {\r
+    public java.lang.String getBgColour(\r
+    ) {\r
         return this._bgColour;\r
-    } //-- java.lang.String getBgColour() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'centreColumnLabels'.\r
+     * \r
+     * @return the value of field 'CentreColumnLabels'.\r
+     */\r
+    public boolean getCentreColumnLabels(\r
+    ) {\r
+        return this._centreColumnLabels;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'consThreshold'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'consThreshold'.\r
+     * @return the value of field 'ConsThreshold'.\r
      */\r
-    public int getConsThreshold()\r
-    {\r
+    public int getConsThreshold(\r
+    ) {\r
         return this._consThreshold;\r
-    } //-- int getConsThreshold() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'conservationSelected'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'conservationSelected'.\r
+     * @return the value of field 'ConservationSelected'.\r
      */\r
-    public boolean getConservationSelected()\r
-    {\r
+    public boolean getConservationSelected(\r
+    ) {\r
         return this._conservationSelected;\r
-    } //-- boolean getConservationSelected() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followHighlight'.\r
+     * \r
+     * @return the value of field 'FollowHighlight'.\r
+     */\r
+    public boolean getFollowHighlight(\r
+    ) {\r
+        return this._followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followSelection'.\r
+     * \r
+     * @return the value of field 'FollowSelection'.\r
+     */\r
+    public boolean getFollowSelection(\r
+    ) {\r
+        return this._followSelection;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'fontName'.\r
      * \r
-     * @return String\r
-     * @return the value of field 'fontName'.\r
+     * @return the value of field 'FontName'.\r
      */\r
-    public java.lang.String getFontName()\r
-    {\r
+    public java.lang.String getFontName(\r
+    ) {\r
         return this._fontName;\r
-    } //-- java.lang.String getFontName() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'fontSize'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'fontSize'.\r
+     * @return the value of field 'FontSize'.\r
      */\r
-    public int getFontSize()\r
-    {\r
+    public int getFontSize(\r
+    ) {\r
         return this._fontSize;\r
-    } //-- int getFontSize() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'fontStyle'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'fontStyle'.\r
+     * @return the value of field 'FontStyle'.\r
      */\r
-    public int getFontStyle()\r
-    {\r
+    public int getFontStyle(\r
+    ) {\r
         return this._fontStyle;\r
-    } //-- int getFontStyle() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'gatheredViews'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'gatheredViews'.\r
+     * @return the value of field 'GatheredViews'.\r
      */\r
-    public boolean getGatheredViews()\r
-    {\r
+    public boolean getGatheredViews(\r
+    ) {\r
         return this._gatheredViews;\r
-    } //-- boolean getGatheredViews() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'height'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'height'.\r
+     * @return the value of field 'Height'.\r
      */\r
-    public int getHeight()\r
-    {\r
+    public int getHeight(\r
+    ) {\r
         return this._height;\r
-    } //-- int getHeight() \r
+    }\r
 \r
     /**\r
-     * Method getHiddenColumns\r
-     * \r
-     * \r
+     * Method getHiddenColumns.\r
      * \r
      * @param index\r
-     * @return HiddenColumns\r
-     */\r
-    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        //-- check bounds for index\r
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
-            throw new IndexOutOfBoundsException();\r
+     * @throws java.lang.IndexOutOfBoundsException if the index\r
+     * given is outside the bounds of the collection\r
+     * @return the value of the\r
+     * jalview.schemabinding.version2.HiddenColumns at the given\r
+     * index\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(\r
+            final int index)\r
+    throws java.lang.IndexOutOfBoundsException {\r
+        // check bounds for index\r
+        if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+            throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
         }\r
         \r
-        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
-    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);\r
+    }\r
 \r
     /**\r
-     * Method getHiddenColumns\r
+     * Method getHiddenColumns.Returns the contents of the\r
+     * collection in an Array.  <p>Note:  Just in case the\r
+     * collection contents are changing in another thread, we pass\r
+     * a 0-length Array of the correct type into the API call. \r
+     * This way we <i>know</i> that the Array returned is of\r
+     * exactly the correct length.\r
      * \r
-     * \r
-     * \r
-     * @return HiddenColumns\r
+     * @return this collection as an Array\r
      */\r
-    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
-    {\r
-        int size = _hiddenColumnsList.size();\r
-        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
-        for (int index = 0; index < size; index++) {\r
-            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
-        }\r
-        return mArray;\r
-    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(\r
+    ) {\r
+        jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];\r
+        return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);\r
+    }\r
 \r
     /**\r
-     * Method getHiddenColumnsCount\r
+     * Method getHiddenColumnsCount.\r
      * \r
+     * @return the size of this collection\r
+     */\r
+    public int getHiddenColumnsCount(\r
+    ) {\r
+        return this._hiddenColumnsList.size();\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'id'. The field 'id' has the\r
+     * following description: unique id used by jalview to\r
+     * synchronize between stored and instantiated views\r
+     *  \r
      * \r
+     * @return the value of field 'Id'.\r
+     */\r
+    public java.lang.String getId(\r
+    ) {\r
+        return this._id;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
      * \r
-     * @return int\r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
      */\r
-    public int getHiddenColumnsCount()\r
-    {\r
-        return _hiddenColumnsList.size();\r
-    } //-- int getHiddenColumnsCount() \r
+    public boolean getIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'pidSelected'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'pidSelected'.\r
+     * @return the value of field 'PidSelected'.\r
      */\r
-    public boolean getPidSelected()\r
-    {\r
+    public boolean getPidSelected(\r
+    ) {\r
         return this._pidSelected;\r
-    } //-- boolean getPidSelected() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'pidThreshold'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'pidThreshold'.\r
+     * @return the value of field 'PidThreshold'.\r
      */\r
-    public int getPidThreshold()\r
-    {\r
+    public int getPidThreshold(\r
+    ) {\r
         return this._pidThreshold;\r
-    } //-- int getPidThreshold() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'renderGaps'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'renderGaps'.\r
+     * @return the value of field 'RenderGaps'.\r
      */\r
-    public boolean getRenderGaps()\r
-    {\r
+    public boolean getRenderGaps(\r
+    ) {\r
         return this._renderGaps;\r
-    } //-- boolean getRenderGaps() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'rightAlignIds'.\r
+     * \r
+     * @return the value of field 'RightAlignIds'.\r
+     */\r
+    public boolean getRightAlignIds(\r
+    ) {\r
+        return this._rightAlignIds;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'sequenceSetId'.\r
      * \r
-     * @return String\r
-     * @return the value of field 'sequenceSetId'.\r
+     * @return the value of field 'SequenceSetId'.\r
      */\r
-    public java.lang.String getSequenceSetId()\r
-    {\r
+    public java.lang.String getSequenceSetId(\r
+    ) {\r
         return this._sequenceSetId;\r
-    } //-- java.lang.String getSequenceSetId() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showAnnotation'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showAnnotation'.\r
+     * @return the value of field 'ShowAnnotation'.\r
      */\r
-    public boolean getShowAnnotation()\r
-    {\r
+    public boolean getShowAnnotation(\r
+    ) {\r
         return this._showAnnotation;\r
-    } //-- boolean getShowAnnotation() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showBoxes'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showBoxes'.\r
+     * @return the value of field 'ShowBoxes'.\r
      */\r
-    public boolean getShowBoxes()\r
-    {\r
+    public boolean getShowBoxes(\r
+    ) {\r
         return this._showBoxes;\r
-    } //-- boolean getShowBoxes() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showColourText'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showColourText'.\r
+     * @return the value of field 'ShowColourText'.\r
      */\r
-    public boolean getShowColourText()\r
-    {\r
+    public boolean getShowColourText(\r
+    ) {\r
         return this._showColourText;\r
-    } //-- boolean getShowColourText() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @return the value of field 'ShowConsensusHistogram'.\r
+     */\r
+    public boolean getShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
 \r
     /**\r
-     * Returns the value of field 'showConservation'.\r
+     * Returns the value of field 'showDbRefTooltip'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showConservation'.\r
+     * @return the value of field 'ShowDbRefTooltip'.\r
      */\r
-    public boolean getShowConservation()\r
-    {\r
-        return this._showConservation;\r
-    } //-- boolean getShowConservation() \r
+    public boolean getShowDbRefTooltip(\r
+    ) {\r
+        return this._showDbRefTooltip;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showFullId'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showFullId'.\r
+     * @return the value of field 'ShowFullId'.\r
      */\r
-    public boolean getShowFullId()\r
-    {\r
+    public boolean getShowFullId(\r
+    ) {\r
         return this._showFullId;\r
-    } //-- boolean getShowFullId() \r
+    }\r
 \r
     /**\r
-     * Returns the value of field 'showIdentity'.\r
+     * Returns the value of field 'showGroupConsensus'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showIdentity'.\r
+     * @return the value of field 'ShowGroupConsensus'.\r
      */\r
-    public boolean getShowIdentity()\r
-    {\r
-        return this._showIdentity;\r
-    } //-- boolean getShowIdentity() \r
+    public boolean getShowGroupConsensus(\r
+    ) {\r
+        return this._showGroupConsensus;\r
+    }\r
 \r
     /**\r
-     * Returns the value of field 'showQuality'.\r
+     * Returns the value of field 'showGroupConservation'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showQuality'.\r
+     * @return the value of field 'ShowGroupConservation'.\r
      */\r
-    public boolean getShowQuality()\r
-    {\r
-        return this._showQuality;\r
-    } //-- boolean getShowQuality() \r
+    public boolean getShowGroupConservation(\r
+    ) {\r
+        return this._showGroupConservation;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showNPfeatureTooltip'.\r
+     * \r
+     * @return the value of field 'ShowNPfeatureTooltip'.\r
+     */\r
+    public boolean getShowNPfeatureTooltip(\r
+    ) {\r
+        return this._showNPfeatureTooltip;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showSequenceFeatures'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showSequenceFeatures'.\r
+     * @return the value of field 'ShowSequenceFeatures'.\r
      */\r
-    public boolean getShowSequenceFeatures()\r
-    {\r
+    public boolean getShowSequenceFeatures(\r
+    ) {\r
         return this._showSequenceFeatures;\r
-    } //-- boolean getShowSequenceFeatures() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showSequenceLogo'.\r
+     * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean getShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'showText'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'showText'.\r
+     * @return the value of field 'ShowText'.\r
      */\r
-    public boolean getShowText()\r
-    {\r
+    public boolean getShowText(\r
+    ) {\r
         return this._showText;\r
-    } //-- boolean getShowText() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean getShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'startRes'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'startRes'.\r
+     * @return the value of field 'StartRes'.\r
      */\r
-    public int getStartRes()\r
-    {\r
+    public int getStartRes(\r
+    ) {\r
         return this._startRes;\r
-    } //-- int getStartRes() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'startSeq'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'startSeq'.\r
+     * @return the value of field 'StartSeq'.\r
      */\r
-    public int getStartSeq()\r
-    {\r
+    public int getStartSeq(\r
+    ) {\r
         return this._startSeq;\r
-    } //-- int getStartSeq() \r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'textCol1'.\r
+     * \r
+     * @return the value of field 'TextCol1'.\r
+     */\r
+    public int getTextCol1(\r
+    ) {\r
+        return this._textCol1;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'textCol2'.\r
+     * \r
+     * @return the value of field 'TextCol2'.\r
+     */\r
+    public int getTextCol2(\r
+    ) {\r
+        return this._textCol2;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'textColThreshold'.\r
+     * \r
+     * @return the value of field 'TextColThreshold'.\r
+     */\r
+    public int getTextColThreshold(\r
+    ) {\r
+        return this._textColThreshold;\r
+    }\r
 \r
     /**\r
      * Returns the value of field 'title'.\r
      * \r
-     * @return String\r
-     * @return the value of field 'title'.\r
+     * @return the value of field 'Title'.\r
      */\r
-    public java.lang.String getTitle()\r
-    {\r
+    public java.lang.String getTitle(\r
+    ) {\r
         return this._title;\r
-    } //-- java.lang.String getTitle() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'viewName'.\r
      * \r
-     * @return String\r
-     * @return the value of field 'viewName'.\r
+     * @return the value of field 'ViewName'.\r
      */\r
-    public java.lang.String getViewName()\r
-    {\r
+    public java.lang.String getViewName(\r
+    ) {\r
         return this._viewName;\r
-    } //-- java.lang.String getViewName() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'width'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'width'.\r
+     * @return the value of field 'Width'.\r
      */\r
-    public int getWidth()\r
-    {\r
+    public int getWidth(\r
+    ) {\r
         return this._width;\r
-    } //-- int getWidth() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'wrapAlignment'.\r
      * \r
-     * @return boolean\r
-     * @return the value of field 'wrapAlignment'.\r
+     * @return the value of field 'WrapAlignment'.\r
      */\r
-    public boolean getWrapAlignment()\r
-    {\r
+    public boolean getWrapAlignment(\r
+    ) {\r
         return this._wrapAlignment;\r
-    } //-- boolean getWrapAlignment() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'xpos'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'xpos'.\r
+     * @return the value of field 'Xpos'.\r
      */\r
-    public int getXpos()\r
-    {\r
+    public int getXpos(\r
+    ) {\r
         return this._xpos;\r
-    } //-- int getXpos() \r
+    }\r
 \r
     /**\r
      * Returns the value of field 'ypos'.\r
      * \r
-     * @return int\r
-     * @return the value of field 'ypos'.\r
+     * @return the value of field 'Ypos'.\r
      */\r
-    public int getYpos()\r
-    {\r
+    public int getYpos(\r
+    ) {\r
         return this._ypos;\r
-    } //-- int getYpos() \r
+    }\r
 \r
     /**\r
-     * Method hasConsThreshold\r
-     * \r
+     * Method hasCentreColumnLabels.\r
      * \r
+     * @return true if at least one CentreColumnLabels has been adde\r
+     */\r
+    public boolean hasCentreColumnLabels(\r
+    ) {\r
+        return this._has_centreColumnLabels;\r
+    }\r
+\r
+    /**\r
+     * Method hasConsThreshold.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ConsThreshold has been added\r
      */\r
-    public boolean hasConsThreshold()\r
-    {\r
+    public boolean hasConsThreshold(\r
+    ) {\r
         return this._has_consThreshold;\r
-    } //-- boolean hasConsThreshold() \r
+    }\r
 \r
     /**\r
-     * Method hasConservationSelected\r
-     * \r
-     * \r
+     * Method hasConservationSelected.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ConservationSelected has been\r
+     * added\r
      */\r
-    public boolean hasConservationSelected()\r
-    {\r
+    public boolean hasConservationSelected(\r
+    ) {\r
         return this._has_conservationSelected;\r
-    } //-- boolean hasConservationSelected() \r
+    }\r
 \r
     /**\r
-     * Method hasFontSize\r
+     * Method hasFollowHighlight.\r
      * \r
+     * @return true if at least one FollowHighlight has been added\r
+     */\r
+    public boolean hasFollowHighlight(\r
+    ) {\r
+        return this._has_followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Method hasFollowSelection.\r
      * \r
+     * @return true if at least one FollowSelection has been added\r
+     */\r
+    public boolean hasFollowSelection(\r
+    ) {\r
+        return this._has_followSelection;\r
+    }\r
+\r
+    /**\r
+     * Method hasFontSize.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one FontSize has been added\r
      */\r
-    public boolean hasFontSize()\r
-    {\r
+    public boolean hasFontSize(\r
+    ) {\r
         return this._has_fontSize;\r
-    } //-- boolean hasFontSize() \r
+    }\r
 \r
     /**\r
-     * Method hasFontStyle\r
-     * \r
+     * Method hasFontStyle.\r
      * \r
-     * \r
-     * @return boolean\r
+     * @return true if at least one FontStyle has been added\r
      */\r
-    public boolean hasFontStyle()\r
-    {\r
+    public boolean hasFontStyle(\r
+    ) {\r
         return this._has_fontStyle;\r
-    } //-- boolean hasFontStyle() \r
+    }\r
 \r
     /**\r
-     * Method hasGatheredViews\r
-     * \r
-     * \r
+     * Method hasGatheredViews.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one GatheredViews has been added\r
      */\r
-    public boolean hasGatheredViews()\r
-    {\r
+    public boolean hasGatheredViews(\r
+    ) {\r
         return this._has_gatheredViews;\r
-    } //-- boolean hasGatheredViews() \r
+    }\r
 \r
     /**\r
-     * Method hasHeight\r
+     * Method hasHeight.\r
      * \r
-     * \r
-     * \r
-     * @return boolean\r
+     * @return true if at least one Height has been added\r
      */\r
-    public boolean hasHeight()\r
-    {\r
+    public boolean hasHeight(\r
+    ) {\r
         return this._has_height;\r
-    } //-- boolean hasHeight() \r
+    }\r
 \r
     /**\r
-     * Method hasPidSelected\r
-     * \r
+     * Method hasIgnoreGapsinConsensus.\r
      * \r
+     * @return true if at least one IgnoreGapsinConsensus has been\r
+     * added\r
+     */\r
+    public boolean hasIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._has_ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
+     * Method hasPidSelected.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one PidSelected has been added\r
      */\r
-    public boolean hasPidSelected()\r
-    {\r
+    public boolean hasPidSelected(\r
+    ) {\r
         return this._has_pidSelected;\r
-    } //-- boolean hasPidSelected() \r
+    }\r
 \r
     /**\r
-     * Method hasPidThreshold\r
+     * Method hasPidThreshold.\r
      * \r
-     * \r
-     * \r
-     * @return boolean\r
+     * @return true if at least one PidThreshold has been added\r
      */\r
-    public boolean hasPidThreshold()\r
-    {\r
+    public boolean hasPidThreshold(\r
+    ) {\r
         return this._has_pidThreshold;\r
-    } //-- boolean hasPidThreshold() \r
+    }\r
 \r
     /**\r
-     * Method hasRenderGaps\r
-     * \r
-     * \r
+     * Method hasRenderGaps.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one RenderGaps has been added\r
      */\r
-    public boolean hasRenderGaps()\r
-    {\r
+    public boolean hasRenderGaps(\r
+    ) {\r
         return this._has_renderGaps;\r
-    } //-- boolean hasRenderGaps() \r
+    }\r
 \r
     /**\r
-     * Method hasShowAnnotation\r
-     * \r
+     * Method hasRightAlignIds.\r
      * \r
+     * @return true if at least one RightAlignIds has been added\r
+     */\r
+    public boolean hasRightAlignIds(\r
+    ) {\r
+        return this._has_rightAlignIds;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowAnnotation.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ShowAnnotation has been added\r
      */\r
-    public boolean hasShowAnnotation()\r
-    {\r
+    public boolean hasShowAnnotation(\r
+    ) {\r
         return this._has_showAnnotation;\r
-    } //-- boolean hasShowAnnotation() \r
+    }\r
 \r
     /**\r
-     * Method hasShowBoxes\r
-     * \r
+     * Method hasShowBoxes.\r
      * \r
-     * \r
-     * @return boolean\r
+     * @return true if at least one ShowBoxes has been added\r
      */\r
-    public boolean hasShowBoxes()\r
-    {\r
+    public boolean hasShowBoxes(\r
+    ) {\r
         return this._has_showBoxes;\r
-    } //-- boolean hasShowBoxes() \r
+    }\r
 \r
     /**\r
-     * Method hasShowColourText\r
+     * Method hasShowColourText.\r
      * \r
+     * @return true if at least one ShowColourText has been added\r
+     */\r
+    public boolean hasShowColourText(\r
+    ) {\r
+        return this._has_showColourText;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowConsensusHistogram.\r
      * \r
+     * @return true if at least one ShowConsensusHistogram has been\r
+     * added\r
+     */\r
+    public boolean hasShowConsensusHistogram(\r
+    ) {\r
+        return this._has_showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowDbRefTooltip.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ShowDbRefTooltip has been added\r
      */\r
-    public boolean hasShowColourText()\r
-    {\r
-        return this._has_showColourText;\r
-    } //-- boolean hasShowColourText() \r
+    public boolean hasShowDbRefTooltip(\r
+    ) {\r
+        return this._has_showDbRefTooltip;\r
+    }\r
 \r
     /**\r
-     * Method hasShowConservation\r
+     * Method hasShowFullId.\r
      * \r
+     * @return true if at least one ShowFullId has been added\r
+     */\r
+    public boolean hasShowFullId(\r
+    ) {\r
+        return this._has_showFullId;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowGroupConsensus.\r
      * \r
+     * @return true if at least one ShowGroupConsensus has been adde\r
+     */\r
+    public boolean hasShowGroupConsensus(\r
+    ) {\r
+        return this._has_showGroupConsensus;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowGroupConservation.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ShowGroupConservation has been\r
+     * added\r
      */\r
-    public boolean hasShowConservation()\r
-    {\r
-        return this._has_showConservation;\r
-    } //-- boolean hasShowConservation() \r
+    public boolean hasShowGroupConservation(\r
+    ) {\r
+        return this._has_showGroupConservation;\r
+    }\r
 \r
     /**\r
-     * Method hasShowFullId\r
+     * Method hasShowNPfeatureTooltip.\r
      * \r
+     * @return true if at least one ShowNPfeatureTooltip has been\r
+     * added\r
+     */\r
+    public boolean hasShowNPfeatureTooltip(\r
+    ) {\r
+        return this._has_showNPfeatureTooltip;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowSequenceFeatures.\r
      * \r
+     * @return true if at least one ShowSequenceFeatures has been\r
+     * added\r
+     */\r
+    public boolean hasShowSequenceFeatures(\r
+    ) {\r
+        return this._has_showSequenceFeatures;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowSequenceLogo.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one ShowSequenceLogo has been added\r
      */\r
-    public boolean hasShowFullId()\r
-    {\r
-        return this._has_showFullId;\r
-    } //-- boolean hasShowFullId() \r
+    public boolean hasShowSequenceLogo(\r
+    ) {\r
+        return this._has_showSequenceLogo;\r
+    }\r
 \r
     /**\r
-     * Method hasShowIdentity\r
+     * Method hasShowText.\r
      * \r
+     * @return true if at least one ShowText has been added\r
+     */\r
+    public boolean hasShowText(\r
+    ) {\r
+        return this._has_showText;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowUnconserved.\r
      * \r
+     * @return true if at least one ShowUnconserved has been added\r
+     */\r
+    public boolean hasShowUnconserved(\r
+    ) {\r
+        return this._has_showUnconserved;\r
+    }\r
+\r
+    /**\r
+     * Method hasStartRes.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one StartRes has been added\r
      */\r
-    public boolean hasShowIdentity()\r
-    {\r
-        return this._has_showIdentity;\r
-    } //-- boolean hasShowIdentity() \r
+    public boolean hasStartRes(\r
+    ) {\r
+        return this._has_startRes;\r
+    }\r
 \r
     /**\r
-     * Method hasShowQuality\r
+     * Method hasStartSeq.\r
      * \r
+     * @return true if at least one StartSeq has been added\r
+     */\r
+    public boolean hasStartSeq(\r
+    ) {\r
+        return this._has_startSeq;\r
+    }\r
+\r
+    /**\r
+     * Method hasTextCol1.\r
      * \r
+     * @return true if at least one TextCol1 has been added\r
+     */\r
+    public boolean hasTextCol1(\r
+    ) {\r
+        return this._has_textCol1;\r
+    }\r
+\r
+    /**\r
+     * Method hasTextCol2.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one TextCol2 has been added\r
      */\r
-    public boolean hasShowQuality()\r
-    {\r
-        return this._has_showQuality;\r
-    } //-- boolean hasShowQuality() \r
+    public boolean hasTextCol2(\r
+    ) {\r
+        return this._has_textCol2;\r
+    }\r
 \r
     /**\r
-     * Method hasShowSequenceFeatures\r
+     * Method hasTextColThreshold.\r
      * \r
+     * @return true if at least one TextColThreshold has been added\r
+     */\r
+    public boolean hasTextColThreshold(\r
+    ) {\r
+        return this._has_textColThreshold;\r
+    }\r
+\r
+    /**\r
+     * Method hasWidth.\r
      * \r
+     * @return true if at least one Width has been added\r
+     */\r
+    public boolean hasWidth(\r
+    ) {\r
+        return this._has_width;\r
+    }\r
+\r
+    /**\r
+     * Method hasWrapAlignment.\r
      * \r
-     * @return boolean\r
+     * @return true if at least one WrapAlignment has been added\r
      */\r
-    public boolean hasShowSequenceFeatures()\r
-    {\r
-        return this._has_showSequenceFeatures;\r
-    } //-- boolean hasShowSequenceFeatures() \r
+    public boolean hasWrapAlignment(\r
+    ) {\r
+        return this._has_wrapAlignment;\r
+    }\r
 \r
     /**\r
-     * Method hasShowText\r
+     * Method hasXpos.\r
      * \r
+     * @return true if at least one Xpos has been added\r
+     */\r
+    public boolean hasXpos(\r
+    ) {\r
+        return this._has_xpos;\r
+    }\r
+\r
+    /**\r
+     * Method hasYpos.\r
      * \r
+     * @return true if at least one Ypos has been added\r
+     */\r
+    public boolean hasYpos(\r
+    ) {\r
+        return this._has_ypos;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'centreColumnLabels'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'CentreColumnLabels'.\r
      */\r
-    public boolean hasShowText()\r
-    {\r
-        return this._has_showText;\r
-    } //-- boolean hasShowText() \r
+    public boolean isCentreColumnLabels(\r
+    ) {\r
+        return this._centreColumnLabels;\r
+    }\r
 \r
     /**\r
-     * Method hasStartRes\r
+     * Returns the value of field 'conservationSelected'.\r
      * \r
+     * @return the value of field 'ConservationSelected'.\r
+     */\r
+    public boolean isConservationSelected(\r
+    ) {\r
+        return this._conservationSelected;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followHighlight'.\r
      * \r
+     * @return the value of field 'FollowHighlight'.\r
+     */\r
+    public boolean isFollowHighlight(\r
+    ) {\r
+        return this._followHighlight;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'followSelection'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'FollowSelection'.\r
      */\r
-    public boolean hasStartRes()\r
-    {\r
-        return this._has_startRes;\r
-    } //-- boolean hasStartRes() \r
+    public boolean isFollowSelection(\r
+    ) {\r
+        return this._followSelection;\r
+    }\r
 \r
     /**\r
-     * Method hasStartSeq\r
+     * Returns the value of field 'gatheredViews'.\r
      * \r
+     * @return the value of field 'GatheredViews'.\r
+     */\r
+    public boolean isGatheredViews(\r
+    ) {\r
+        return this._gatheredViews;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
      * \r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
+     */\r
+    public boolean isIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'pidSelected'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'PidSelected'.\r
      */\r
-    public boolean hasStartSeq()\r
-    {\r
-        return this._has_startSeq;\r
-    } //-- boolean hasStartSeq() \r
+    public boolean isPidSelected(\r
+    ) {\r
+        return this._pidSelected;\r
+    }\r
 \r
     /**\r
-     * Method hasWidth\r
+     * Returns the value of field 'renderGaps'.\r
      * \r
+     * @return the value of field 'RenderGaps'.\r
+     */\r
+    public boolean isRenderGaps(\r
+    ) {\r
+        return this._renderGaps;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'rightAlignIds'.\r
      * \r
+     * @return the value of field 'RightAlignIds'.\r
+     */\r
+    public boolean isRightAlignIds(\r
+    ) {\r
+        return this._rightAlignIds;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showAnnotation'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'ShowAnnotation'.\r
      */\r
-    public boolean hasWidth()\r
-    {\r
-        return this._has_width;\r
-    } //-- boolean hasWidth() \r
+    public boolean isShowAnnotation(\r
+    ) {\r
+        return this._showAnnotation;\r
+    }\r
 \r
     /**\r
-     * Method hasWrapAlignment\r
+     * Returns the value of field 'showBoxes'.\r
      * \r
+     * @return the value of field 'ShowBoxes'.\r
+     */\r
+    public boolean isShowBoxes(\r
+    ) {\r
+        return this._showBoxes;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showColourText'.\r
      * \r
+     * @return the value of field 'ShowColourText'.\r
+     */\r
+    public boolean isShowColourText(\r
+    ) {\r
+        return this._showColourText;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'ShowConsensusHistogram'.\r
      */\r
-    public boolean hasWrapAlignment()\r
-    {\r
-        return this._has_wrapAlignment;\r
-    } //-- boolean hasWrapAlignment() \r
+    public boolean isShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
 \r
     /**\r
-     * Method hasXpos\r
+     * Returns the value of field 'showDbRefTooltip'.\r
      * \r
+     * @return the value of field 'ShowDbRefTooltip'.\r
+     */\r
+    public boolean isShowDbRefTooltip(\r
+    ) {\r
+        return this._showDbRefTooltip;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showFullId'.\r
      * \r
+     * @return the value of field 'ShowFullId'.\r
+     */\r
+    public boolean isShowFullId(\r
+    ) {\r
+        return this._showFullId;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showGroupConsensus'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'ShowGroupConsensus'.\r
      */\r
-    public boolean hasXpos()\r
-    {\r
-        return this._has_xpos;\r
-    } //-- boolean hasXpos() \r
+    public boolean isShowGroupConsensus(\r
+    ) {\r
+        return this._showGroupConsensus;\r
+    }\r
 \r
     /**\r
-     * Method hasYpos\r
+     * Returns the value of field 'showGroupConservation'.\r
      * \r
+     * @return the value of field 'ShowGroupConservation'.\r
+     */\r
+    public boolean isShowGroupConservation(\r
+    ) {\r
+        return this._showGroupConservation;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showNPfeatureTooltip'.\r
      * \r
+     * @return the value of field 'ShowNPfeatureTooltip'.\r
+     */\r
+    public boolean isShowNPfeatureTooltip(\r
+    ) {\r
+        return this._showNPfeatureTooltip;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showSequenceFeatures'.\r
      * \r
-     * @return boolean\r
+     * @return the value of field 'ShowSequenceFeatures'.\r
      */\r
-    public boolean hasYpos()\r
-    {\r
-        return this._has_ypos;\r
-    } //-- boolean hasYpos() \r
+    public boolean isShowSequenceFeatures(\r
+    ) {\r
+        return this._showSequenceFeatures;\r
+    }\r
 \r
     /**\r
-     * Method isValid\r
+     * Returns the value of field 'showSequenceLogo'.\r
      * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean isShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showText'.\r
+     * \r
+     * @return the value of field 'ShowText'.\r
+     */\r
+    public boolean isShowText(\r
+    ) {\r
+        return this._showText;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showUnconserved'.\r
      * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean isShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
+     * Method isValid.\r
      * \r
-     * @return boolean\r
+     * @return true if this object is valid according to the schema\r
      */\r
-    public boolean isValid()\r
-    {\r
+    public boolean isValid(\r
+    ) {\r
         try {\r
             validate();\r
-        }\r
-        catch (org.exolab.castor.xml.ValidationException vex) {\r
+        } catch (org.exolab.castor.xml.ValidationException vex) {\r
             return false;\r
         }\r
         return true;\r
-    } //-- boolean isValid() \r
+    }\r
 \r
     /**\r
-     * Method marshal\r
+     * Returns the value of field 'wrapAlignment'.\r
      * \r
+     * @return the value of field 'WrapAlignment'.\r
+     */\r
+    public boolean isWrapAlignment(\r
+    ) {\r
+        return this._wrapAlignment;\r
+    }\r
+\r
+    /**\r
      * \r
      * \r
      * @param out\r
-     */\r
-    public void marshal(java.io.Writer out)\r
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
-        \r
+     * @throws org.exolab.castor.xml.MarshalException if object is\r
+     * null or if any SAXException is thrown during marshaling\r
+     * @throws org.exolab.castor.xml.ValidationException if this\r
+     * object is an invalid instance according to the schema\r
+     */\r
+    public void marshal(\r
+            final java.io.Writer out)\r
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
         Marshaller.marshal(this, out);\r
-    } //-- void marshal(java.io.Writer) \r
+    }\r
 \r
     /**\r
-     * Method marshal\r
-     * \r
      * \r
      * \r
      * @param handler\r
-     */\r
-    public void marshal(org.xml.sax.ContentHandler handler)\r
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
-        \r
+     * @throws java.io.IOException if an IOException occurs during\r
+     * marshaling\r
+     * @throws org.exolab.castor.xml.ValidationException if this\r
+     * object is an invalid instance according to the schema\r
+     * @throws org.exolab.castor.xml.MarshalException if object is\r
+     * null or if any SAXException is thrown during marshaling\r
+     */\r
+    public void marshal(\r
+            final org.xml.sax.ContentHandler handler)\r
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
         Marshaller.marshal(this, handler);\r
-    } //-- void marshal(org.xml.sax.ContentHandler) \r
+    }\r
 \r
     /**\r
-     * Method removeAllHiddenColumns\r
-     * \r
      */\r
-    public void removeAllHiddenColumns()\r
-    {\r
-        _hiddenColumnsList.removeAllElements();\r
-    } //-- void removeAllHiddenColumns() \r
+    public void removeAllHiddenColumns(\r
+    ) {\r
+        this._hiddenColumnsList.clear();\r
+    }\r
 \r
     /**\r
-     * Method removeHiddenColumns\r
-     * \r
+     * Method removeHiddenColumns.\r
      * \r
+     * @param vHiddenColumns\r
+     * @return true if the object was removed from the collection.\r
+     */\r
+    public boolean removeHiddenColumns(\r
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {\r
+        boolean removed = _hiddenColumnsList.remove(vHiddenColumns);\r
+        return removed;\r
+    }\r
+\r
+    /**\r
+     * Method removeHiddenColumnsAt.\r
      * \r
      * @param index\r
-     * @return HiddenColumns\r
+     * @return the element removed from the collection\r
      */\r
-    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
-    {\r
-        java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
-        _hiddenColumnsList.removeElementAt(index);\r
+    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(\r
+            final int index) {\r
+        java.lang.Object obj = this._hiddenColumnsList.remove(index);\r
         return (jalview.schemabinding.version2.HiddenColumns) obj;\r
-    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'annotationColours'.\r
@@ -1322,31 +1894,43 @@ public class Viewport implements java.io.Serializable {
      * @param annotationColours the value of field\r
      * 'annotationColours'.\r
      */\r
-    public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)\r
-    {\r
+    public void setAnnotationColours(\r
+            final jalview.schemabinding.version2.AnnotationColours annotationColours) {\r
         this._annotationColours = annotationColours;\r
-    } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'bgColour'.\r
      * \r
      * @param bgColour the value of field 'bgColour'.\r
      */\r
-    public void setBgColour(java.lang.String bgColour)\r
-    {\r
+    public void setBgColour(\r
+            final java.lang.String bgColour) {\r
         this._bgColour = bgColour;\r
-    } //-- void setBgColour(java.lang.String) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'centreColumnLabels'.\r
+     * \r
+     * @param centreColumnLabels the value of field\r
+     * 'centreColumnLabels'.\r
+     */\r
+    public void setCentreColumnLabels(\r
+            final boolean centreColumnLabels) {\r
+        this._centreColumnLabels = centreColumnLabels;\r
+        this._has_centreColumnLabels = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'consThreshold'.\r
      * \r
      * @param consThreshold the value of field 'consThreshold'.\r
      */\r
-    public void setConsThreshold(int consThreshold)\r
-    {\r
+    public void setConsThreshold(\r
+            final int consThreshold) {\r
         this._consThreshold = consThreshold;\r
         this._has_consThreshold = true;\r
-    } //-- void setConsThreshold(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'conservationSelected'.\r
@@ -1354,219 +1938,304 @@ public class Viewport implements java.io.Serializable {
      * @param conservationSelected the value of field\r
      * 'conservationSelected'.\r
      */\r
-    public void setConservationSelected(boolean conservationSelected)\r
-    {\r
+    public void setConservationSelected(\r
+            final boolean conservationSelected) {\r
         this._conservationSelected = conservationSelected;\r
         this._has_conservationSelected = true;\r
-    } //-- void setConservationSelected(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'followHighlight'.\r
+     * \r
+     * @param followHighlight the value of field 'followHighlight'.\r
+     */\r
+    public void setFollowHighlight(\r
+            final boolean followHighlight) {\r
+        this._followHighlight = followHighlight;\r
+        this._has_followHighlight = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'followSelection'.\r
+     * \r
+     * @param followSelection the value of field 'followSelection'.\r
+     */\r
+    public void setFollowSelection(\r
+            final boolean followSelection) {\r
+        this._followSelection = followSelection;\r
+        this._has_followSelection = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'fontName'.\r
      * \r
      * @param fontName the value of field 'fontName'.\r
      */\r
-    public void setFontName(java.lang.String fontName)\r
-    {\r
+    public void setFontName(\r
+            final java.lang.String fontName) {\r
         this._fontName = fontName;\r
-    } //-- void setFontName(java.lang.String) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'fontSize'.\r
      * \r
      * @param fontSize the value of field 'fontSize'.\r
      */\r
-    public void setFontSize(int fontSize)\r
-    {\r
+    public void setFontSize(\r
+            final int fontSize) {\r
         this._fontSize = fontSize;\r
         this._has_fontSize = true;\r
-    } //-- void setFontSize(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'fontStyle'.\r
      * \r
      * @param fontStyle the value of field 'fontStyle'.\r
      */\r
-    public void setFontStyle(int fontStyle)\r
-    {\r
+    public void setFontStyle(\r
+            final int fontStyle) {\r
         this._fontStyle = fontStyle;\r
         this._has_fontStyle = true;\r
-    } //-- void setFontStyle(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'gatheredViews'.\r
      * \r
      * @param gatheredViews the value of field 'gatheredViews'.\r
      */\r
-    public void setGatheredViews(boolean gatheredViews)\r
-    {\r
+    public void setGatheredViews(\r
+            final boolean gatheredViews) {\r
         this._gatheredViews = gatheredViews;\r
         this._has_gatheredViews = true;\r
-    } //-- void setGatheredViews(boolean) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'height'.\r
      * \r
      * @param height the value of field 'height'.\r
      */\r
-    public void setHeight(int height)\r
-    {\r
+    public void setHeight(\r
+            final int height) {\r
         this._height = height;\r
         this._has_height = true;\r
-    } //-- void setHeight(int) \r
+    }\r
 \r
     /**\r
-     * Method setHiddenColumns\r
-     * \r
      * \r
      * \r
      * @param index\r
      * @param vHiddenColumns\r
-     */\r
-    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        //-- check bounds for index\r
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
-            throw new IndexOutOfBoundsException();\r
+     * @throws java.lang.IndexOutOfBoundsException if the index\r
+     * given is outside the bounds of the collection\r
+     */\r
+    public void setHiddenColumns(\r
+            final int index,\r
+            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+    throws java.lang.IndexOutOfBoundsException {\r
+        // check bounds for index\r
+        if (index < 0 || index >= this._hiddenColumnsList.size()) {\r
+            throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");\r
         }\r
-        _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
-    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+        \r
+        this._hiddenColumnsList.set(index, vHiddenColumns);\r
+    }\r
 \r
     /**\r
-     * Method setHiddenColumns\r
-     * \r
      * \r
      * \r
-     * @param hiddenColumnsArray\r
+     * @param vHiddenColumnsArray\r
      */\r
-    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
-    {\r
+    public void setHiddenColumns(\r
+            final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {\r
         //-- copy array\r
-        _hiddenColumnsList.removeAllElements();\r
-        for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
-            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+        _hiddenColumnsList.clear();\r
+        \r
+        for (int i = 0; i < vHiddenColumnsArray.length; i++) {\r
+                this._hiddenColumnsList.add(vHiddenColumnsArray[i]);\r
         }\r
-    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'id'. The field 'id' has the\r
+     * following description: unique id used by jalview to\r
+     * synchronize between stored and instantiated views\r
+     *  \r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(\r
+            final java.lang.String id) {\r
+        this._id = id;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @param ignoreGapsinConsensus the value of field\r
+     * 'ignoreGapsinConsensus'.\r
+     */\r
+    public void setIgnoreGapsinConsensus(\r
+            final boolean ignoreGapsinConsensus) {\r
+        this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+        this._has_ignoreGapsinConsensus = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'pidSelected'.\r
      * \r
      * @param pidSelected the value of field 'pidSelected'.\r
      */\r
-    public void setPidSelected(boolean pidSelected)\r
-    {\r
+    public void setPidSelected(\r
+            final boolean pidSelected) {\r
         this._pidSelected = pidSelected;\r
         this._has_pidSelected = true;\r
-    } //-- void setPidSelected(boolean) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'pidThreshold'.\r
      * \r
      * @param pidThreshold the value of field 'pidThreshold'.\r
      */\r
-    public void setPidThreshold(int pidThreshold)\r
-    {\r
+    public void setPidThreshold(\r
+            final int pidThreshold) {\r
         this._pidThreshold = pidThreshold;\r
         this._has_pidThreshold = true;\r
-    } //-- void setPidThreshold(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'renderGaps'.\r
      * \r
      * @param renderGaps the value of field 'renderGaps'.\r
      */\r
-    public void setRenderGaps(boolean renderGaps)\r
-    {\r
+    public void setRenderGaps(\r
+            final boolean renderGaps) {\r
         this._renderGaps = renderGaps;\r
         this._has_renderGaps = true;\r
-    } //-- void setRenderGaps(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'rightAlignIds'.\r
+     * \r
+     * @param rightAlignIds the value of field 'rightAlignIds'.\r
+     */\r
+    public void setRightAlignIds(\r
+            final boolean rightAlignIds) {\r
+        this._rightAlignIds = rightAlignIds;\r
+        this._has_rightAlignIds = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'sequenceSetId'.\r
      * \r
      * @param sequenceSetId the value of field 'sequenceSetId'.\r
      */\r
-    public void setSequenceSetId(java.lang.String sequenceSetId)\r
-    {\r
+    public void setSequenceSetId(\r
+            final java.lang.String sequenceSetId) {\r
         this._sequenceSetId = sequenceSetId;\r
-    } //-- void setSequenceSetId(java.lang.String) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showAnnotation'.\r
      * \r
      * @param showAnnotation the value of field 'showAnnotation'.\r
      */\r
-    public void setShowAnnotation(boolean showAnnotation)\r
-    {\r
+    public void setShowAnnotation(\r
+            final boolean showAnnotation) {\r
         this._showAnnotation = showAnnotation;\r
         this._has_showAnnotation = true;\r
-    } //-- void setShowAnnotation(boolean) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showBoxes'.\r
      * \r
      * @param showBoxes the value of field 'showBoxes'.\r
      */\r
-    public void setShowBoxes(boolean showBoxes)\r
-    {\r
+    public void setShowBoxes(\r
+            final boolean showBoxes) {\r
         this._showBoxes = showBoxes;\r
         this._has_showBoxes = true;\r
-    } //-- void setShowBoxes(boolean) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showColourText'.\r
      * \r
      * @param showColourText the value of field 'showColourText'.\r
      */\r
-    public void setShowColourText(boolean showColourText)\r
-    {\r
+    public void setShowColourText(\r
+            final boolean showColourText) {\r
         this._showColourText = showColourText;\r
         this._has_showColourText = true;\r
-    } //-- void setShowColourText(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @param showConsensusHistogram the value of field\r
+     * 'showConsensusHistogram'.\r
+     */\r
+    public void setShowConsensusHistogram(\r
+            final boolean showConsensusHistogram) {\r
+        this._showConsensusHistogram = showConsensusHistogram;\r
+        this._has_showConsensusHistogram = true;\r
+    }\r
 \r
     /**\r
-     * Sets the value of field 'showConservation'.\r
+     * Sets the value of field 'showDbRefTooltip'.\r
      * \r
-     * @param showConservation the value of field 'showConservation'\r
+     * @param showDbRefTooltip the value of field 'showDbRefTooltip'\r
      */\r
-    public void setShowConservation(boolean showConservation)\r
-    {\r
-        this._showConservation = showConservation;\r
-        this._has_showConservation = true;\r
-    } //-- void setShowConservation(boolean) \r
+    public void setShowDbRefTooltip(\r
+            final boolean showDbRefTooltip) {\r
+        this._showDbRefTooltip = showDbRefTooltip;\r
+        this._has_showDbRefTooltip = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showFullId'.\r
      * \r
      * @param showFullId the value of field 'showFullId'.\r
      */\r
-    public void setShowFullId(boolean showFullId)\r
-    {\r
+    public void setShowFullId(\r
+            final boolean showFullId) {\r
         this._showFullId = showFullId;\r
         this._has_showFullId = true;\r
-    } //-- void setShowFullId(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showGroupConsensus'.\r
+     * \r
+     * @param showGroupConsensus the value of field\r
+     * 'showGroupConsensus'.\r
+     */\r
+    public void setShowGroupConsensus(\r
+            final boolean showGroupConsensus) {\r
+        this._showGroupConsensus = showGroupConsensus;\r
+        this._has_showGroupConsensus = true;\r
+    }\r
 \r
     /**\r
-     * Sets the value of field 'showIdentity'.\r
+     * Sets the value of field 'showGroupConservation'.\r
      * \r
-     * @param showIdentity the value of field 'showIdentity'.\r
+     * @param showGroupConservation the value of field\r
+     * 'showGroupConservation'.\r
      */\r
-    public void setShowIdentity(boolean showIdentity)\r
-    {\r
-        this._showIdentity = showIdentity;\r
-        this._has_showIdentity = true;\r
-    } //-- void setShowIdentity(boolean) \r
+    public void setShowGroupConservation(\r
+            final boolean showGroupConservation) {\r
+        this._showGroupConservation = showGroupConservation;\r
+        this._has_showGroupConservation = true;\r
+    }\r
 \r
     /**\r
-     * Sets the value of field 'showQuality'.\r
+     * Sets the value of field 'showNPfeatureTooltip'.\r
      * \r
-     * @param showQuality the value of field 'showQuality'.\r
+     * @param showNPfeatureTooltip the value of field\r
+     * 'showNPfeatureTooltip'.\r
      */\r
-    public void setShowQuality(boolean showQuality)\r
-    {\r
-        this._showQuality = showQuality;\r
-        this._has_showQuality = true;\r
-    } //-- void setShowQuality(boolean) \r
+    public void setShowNPfeatureTooltip(\r
+            final boolean showNPfeatureTooltip) {\r
+        this._showNPfeatureTooltip = showNPfeatureTooltip;\r
+        this._has_showNPfeatureTooltip = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showSequenceFeatures'.\r
@@ -1574,132 +2243,192 @@ public class Viewport implements java.io.Serializable {
      * @param showSequenceFeatures the value of field\r
      * 'showSequenceFeatures'.\r
      */\r
-    public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
-    {\r
+    public void setShowSequenceFeatures(\r
+            final boolean showSequenceFeatures) {\r
         this._showSequenceFeatures = showSequenceFeatures;\r
         this._has_showSequenceFeatures = true;\r
-    } //-- void setShowSequenceFeatures(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showSequenceLogo'.\r
+     * \r
+     * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+     */\r
+    public void setShowSequenceLogo(\r
+            final boolean showSequenceLogo) {\r
+        this._showSequenceLogo = showSequenceLogo;\r
+        this._has_showSequenceLogo = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'showText'.\r
      * \r
      * @param showText the value of field 'showText'.\r
      */\r
-    public void setShowText(boolean showText)\r
-    {\r
+    public void setShowText(\r
+            final boolean showText) {\r
         this._showText = showText;\r
         this._has_showText = true;\r
-    } //-- void setShowText(boolean) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showUnconserved'.\r
+     * \r
+     * @param showUnconserved the value of field 'showUnconserved'.\r
+     */\r
+    public void setShowUnconserved(\r
+            final boolean showUnconserved) {\r
+        this._showUnconserved = showUnconserved;\r
+        this._has_showUnconserved = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'startRes'.\r
      * \r
      * @param startRes the value of field 'startRes'.\r
      */\r
-    public void setStartRes(int startRes)\r
-    {\r
+    public void setStartRes(\r
+            final int startRes) {\r
         this._startRes = startRes;\r
         this._has_startRes = true;\r
-    } //-- void setStartRes(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'startSeq'.\r
      * \r
      * @param startSeq the value of field 'startSeq'.\r
      */\r
-    public void setStartSeq(int startSeq)\r
-    {\r
+    public void setStartSeq(\r
+            final int startSeq) {\r
         this._startSeq = startSeq;\r
         this._has_startSeq = true;\r
-    } //-- void setStartSeq(int) \r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'textCol1'.\r
+     * \r
+     * @param textCol1 the value of field 'textCol1'.\r
+     */\r
+    public void setTextCol1(\r
+            final int textCol1) {\r
+        this._textCol1 = textCol1;\r
+        this._has_textCol1 = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'textCol2'.\r
+     * \r
+     * @param textCol2 the value of field 'textCol2'.\r
+     */\r
+    public void setTextCol2(\r
+            final int textCol2) {\r
+        this._textCol2 = textCol2;\r
+        this._has_textCol2 = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'textColThreshold'.\r
+     * \r
+     * @param textColThreshold the value of field 'textColThreshold'\r
+     */\r
+    public void setTextColThreshold(\r
+            final int textColThreshold) {\r
+        this._textColThreshold = textColThreshold;\r
+        this._has_textColThreshold = true;\r
+    }\r
 \r
     /**\r
      * Sets the value of field 'title'.\r
      * \r
      * @param title the value of field 'title'.\r
      */\r
-    public void setTitle(java.lang.String title)\r
-    {\r
+    public void setTitle(\r
+            final java.lang.String title) {\r
         this._title = title;\r
-    } //-- void setTitle(java.lang.String) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'viewName'.\r
      * \r
      * @param viewName the value of field 'viewName'.\r
      */\r
-    public void setViewName(java.lang.String viewName)\r
-    {\r
+    public void setViewName(\r
+            final java.lang.String viewName) {\r
         this._viewName = viewName;\r
-    } //-- void setViewName(java.lang.String) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'width'.\r
      * \r
      * @param width the value of field 'width'.\r
      */\r
-    public void setWidth(int width)\r
-    {\r
+    public void setWidth(\r
+            final int width) {\r
         this._width = width;\r
         this._has_width = true;\r
-    } //-- void setWidth(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'wrapAlignment'.\r
      * \r
      * @param wrapAlignment the value of field 'wrapAlignment'.\r
      */\r
-    public void setWrapAlignment(boolean wrapAlignment)\r
-    {\r
+    public void setWrapAlignment(\r
+            final boolean wrapAlignment) {\r
         this._wrapAlignment = wrapAlignment;\r
         this._has_wrapAlignment = true;\r
-    } //-- void setWrapAlignment(boolean) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'xpos'.\r
      * \r
      * @param xpos the value of field 'xpos'.\r
      */\r
-    public void setXpos(int xpos)\r
-    {\r
+    public void setXpos(\r
+            final int xpos) {\r
         this._xpos = xpos;\r
         this._has_xpos = true;\r
-    } //-- void setXpos(int) \r
+    }\r
 \r
     /**\r
      * Sets the value of field 'ypos'.\r
      * \r
      * @param ypos the value of field 'ypos'.\r
      */\r
-    public void setYpos(int ypos)\r
-    {\r
+    public void setYpos(\r
+            final int ypos) {\r
         this._ypos = ypos;\r
         this._has_ypos = true;\r
-    } //-- void setYpos(int) \r
+    }\r
 \r
     /**\r
-     * Method unmarshal\r
-     * \r
-     * \r
+     * Method unmarshal.\r
      * \r
      * @param reader\r
-     * @return Object\r
-     */\r
-    public static java.lang.Object unmarshal(java.io.Reader reader)\r
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
-    {\r
+     * @throws org.exolab.castor.xml.MarshalException if object is\r
+     * null or if any SAXException is thrown during marshaling\r
+     * @throws org.exolab.castor.xml.ValidationException if this\r
+     * object is an invalid instance according to the schema\r
+     * @return the unmarshaled\r
+     * jalview.schemabinding.version2.Viewport\r
+     */\r
+    public static jalview.schemabinding.version2.Viewport unmarshal(\r
+            final java.io.Reader reader)\r
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
         return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
-    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+    }\r
 \r
     /**\r
-     * Method validate\r
      * \r
+     * \r
+     * @throws org.exolab.castor.xml.ValidationException if this\r
+     * object is an invalid instance according to the schema\r
      */\r
-    public void validate()\r
-        throws org.exolab.castor.xml.ValidationException\r
-    {\r
+    public void validate(\r
+    )\r
+    throws org.exolab.castor.xml.ValidationException {\r
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
         validator.validate(this);\r
-    } //-- void validate() \r
+    }\r
 \r
 }\r