X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=309e704d3fb2290dae9dd7b3fbb4671b15bc3e22;hb=a95b88b05400d7e841f9523d4c4228c678307654;hp=06eb940abe27440ea2248f7b2814964b8ce6d099;hpb=8def9b1990b937b039d682d6a7b093dcfea130c2;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 06eb940..309e704 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.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 JGroup.
@@ -36,7 +27,7 @@ public class JGroup implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _start
+     * Field _start.
      */
     private int _start;
 
@@ -46,7 +37,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_start;
 
     /**
-     * Field _end
+     * Field _end.
      */
     private int _end;
 
@@ -56,17 +47,17 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_end;
 
     /**
-     * Field _name
+     * Field _name.
      */
     private java.lang.String _name;
 
     /**
-     * Field _colour
+     * Field _colour.
      */
     private java.lang.String _colour;
 
     /**
-     * Field _consThreshold
+     * Field _consThreshold.
      */
     private int _consThreshold;
 
@@ -76,7 +67,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_consThreshold;
 
     /**
-     * Field _pidThreshold
+     * Field _pidThreshold.
      */
     private int _pidThreshold;
 
@@ -86,7 +77,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_pidThreshold;
 
     /**
-     * Field _outlineColour
+     * Field _outlineColour.
      */
     private int _outlineColour;
 
@@ -96,7 +87,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_outlineColour;
 
     /**
-     * Field _displayBoxes
+     * Field _displayBoxes.
      */
     private boolean _displayBoxes;
 
@@ -106,7 +97,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_displayBoxes;
 
     /**
-     * Field _displayText
+     * Field _displayText.
      */
     private boolean _displayText;
 
@@ -116,7 +107,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_displayText;
 
     /**
-     * Field _colourText
+     * Field _colourText.
      */
     private boolean _colourText;
 
@@ -126,7 +117,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_colourText;
 
     /**
-     * Field _textCol1
+     * Field _textCol1.
      */
     private int _textCol1;
 
@@ -136,7 +127,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textCol1;
 
     /**
-     * Field _textCol2
+     * Field _textCol2.
      */
     private int _textCol2;
 
@@ -146,7 +137,7 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textCol2;
 
     /**
-     * Field _textColThreshold
+     * Field _textColThreshold.
      */
     private int _textColThreshold;
 
@@ -156,7 +147,54 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textColThreshold;
 
     /**
-     * Field _seqList
+     * Field _showUnconserved.
+     */
+    private boolean _showUnconserved;
+
+    /**
+     * keeps track of state for field: _showUnconserved
+     */
+    private boolean _has_showUnconserved;
+
+    /**
+     * Field _ignoreGapsinConsensus.
+     */
+    private boolean _ignoreGapsinConsensus = true;
+
+    /**
+     * keeps track of state for field: _ignoreGapsinConsensus
+     */
+    private boolean _has_ignoreGapsinConsensus;
+
+    /**
+     * Field _showConsensusHistogram.
+     */
+    private boolean _showConsensusHistogram = true;
+
+    /**
+     * keeps track of state for field: _showConsensusHistogram
+     */
+    private boolean _has_showConsensusHistogram;
+
+    /**
+     * Field _showSequenceLogo.
+     */
+    private boolean _showSequenceLogo = false;
+
+    /**
+     * keeps track of state for field: _showSequenceLogo
+     */
+    private boolean _has_showSequenceLogo;
+
+    /**
+     * Optional sequence group ID (only needs to be unique for this
+     * alignment)
+     *  
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _seqList.
      */
     private java.util.Vector _seqList;
 
@@ -167,8 +205,8 @@ public class JGroup implements java.io.Serializable {
 
     public JGroup() {
         super();
-        _seqList = new Vector();
-    } //-- jalview.schemabinding.version2.JGroup()
+        this._seqList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -176,734 +214,937 @@ public class JGroup implements java.io.Serializable {
     //-----------/
 
     /**
-     * Method addSeq
-     * 
      * 
      * 
      * @param vSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addSeq(int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.addElement(new java.lang.Integer(vSeq));
-    } //-- void addSeq(int) 
+    public void addSeq(
+            final java.lang.String vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._seqList.addElement(vSeq);
+    }
 
     /**
-     * Method addSeq
-     * 
      * 
      * 
      * @param index
      * @param vSeq
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
      */
-    public void addSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void addSeq(int, int) 
+    public void addSeq(
+            final int index,
+            final java.lang.String vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        this._seqList.add(index, vSeq);
+    }
 
     /**
-     * Method deleteColourText
-     * 
      */
-    public void deleteColourText()
-    {
+    public void deleteColourText(
+    ) {
         this._has_colourText= false;
-    } //-- void deleteColourText() 
+    }
 
     /**
-     * Method deleteConsThreshold
-     * 
      */
-    public void deleteConsThreshold()
-    {
+    public void deleteConsThreshold(
+    ) {
         this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
+    }
 
     /**
-     * Method deleteDisplayBoxes
-     * 
      */
-    public void deleteDisplayBoxes()
-    {
+    public void deleteDisplayBoxes(
+    ) {
         this._has_displayBoxes= false;
-    } //-- void deleteDisplayBoxes() 
+    }
 
     /**
-     * Method deleteDisplayText
-     * 
      */
-    public void deleteDisplayText()
-    {
+    public void deleteDisplayText(
+    ) {
         this._has_displayText= false;
-    } //-- void deleteDisplayText() 
+    }
 
     /**
-     * Method deleteEnd
-     * 
      */
-    public void deleteEnd()
-    {
+    public void deleteEnd(
+    ) {
         this._has_end= false;
-    } //-- void deleteEnd() 
+    }
+
+    /**
+     */
+    public void deleteIgnoreGapsinConsensus(
+    ) {
+        this._has_ignoreGapsinConsensus= false;
+    }
 
     /**
-     * Method deleteOutlineColour
-     * 
      */
-    public void deleteOutlineColour()
-    {
+    public void deleteOutlineColour(
+    ) {
         this._has_outlineColour= false;
-    } //-- void deleteOutlineColour() 
+    }
 
     /**
-     * Method deletePidThreshold
-     * 
      */
-    public void deletePidThreshold()
-    {
+    public void deletePidThreshold(
+    ) {
         this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
+    }
 
     /**
-     * Method deleteStart
-     * 
      */
-    public void deleteStart()
-    {
+    public void deleteShowConsensusHistogram(
+    ) {
+        this._has_showConsensusHistogram= false;
+    }
+
+    /**
+     */
+    public void deleteShowSequenceLogo(
+    ) {
+        this._has_showSequenceLogo= false;
+    }
+
+    /**
+     */
+    public void deleteShowUnconserved(
+    ) {
+        this._has_showUnconserved= false;
+    }
+
+    /**
+     */
+    public void deleteStart(
+    ) {
         this._has_start= false;
-    } //-- void deleteStart() 
+    }
 
     /**
-     * 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 enumerateSeq
-     * 
-     * 
+     * Method enumerateSeq.
      * 
-     * @return Enumeration
+     * @return an Enumeration over all java.lang.String elements
      */
-    public java.util.Enumeration enumerateSeq()
-    {
-        return _seqList.elements();
-    } //-- java.util.Enumeration enumerateSeq() 
+    public java.util.Enumeration enumerateSeq(
+    ) {
+        return this._seqList.elements();
+    }
 
     /**
      * Returns the value of field 'colour'.
      * 
-     * @return String
-     * @return the value of field 'colour'.
+     * @return the value of field 'Colour'.
      */
-    public java.lang.String getColour()
-    {
+    public java.lang.String getColour(
+    ) {
         return this._colour;
-    } //-- java.lang.String getColour() 
+    }
 
     /**
      * Returns the value of field 'colourText'.
      * 
-     * @return boolean
-     * @return the value of field 'colourText'.
+     * @return the value of field 'ColourText'.
      */
-    public boolean getColourText()
-    {
+    public boolean getColourText(
+    ) {
         return this._colourText;
-    } //-- boolean getColourText() 
+    }
 
     /**
      * 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 'displayBoxes'.
      * 
-     * @return boolean
-     * @return the value of field 'displayBoxes'.
+     * @return the value of field 'DisplayBoxes'.
      */
-    public boolean getDisplayBoxes()
-    {
+    public boolean getDisplayBoxes(
+    ) {
         return this._displayBoxes;
-    } //-- boolean getDisplayBoxes() 
+    }
 
     /**
      * Returns the value of field 'displayText'.
      * 
-     * @return boolean
-     * @return the value of field 'displayText'.
+     * @return the value of field 'DisplayText'.
      */
-    public boolean getDisplayText()
-    {
+    public boolean getDisplayText(
+    ) {
         return this._displayText;
-    } //-- boolean getDisplayText() 
+    }
 
     /**
      * Returns the value of field 'end'.
      * 
-     * @return int
-     * @return the value of field 'end'.
+     * @return the value of field 'End'.
      */
-    public int getEnd()
-    {
+    public int getEnd(
+    ) {
         return this._end;
-    } //-- int getEnd() 
+    }
+
+    /**
+     * Returns the value of field 'id'. The field 'id' has the
+     * following description: Optional sequence group ID (only
+     * needs to be unique for this alignment)
+     *  
+     * 
+     * @return the value of field 'Id'.
+     */
+    public java.lang.String getId(
+    ) {
+        return this._id;
+    }
+
+    /**
+     * Returns the value of field 'ignoreGapsinConsensus'.
+     * 
+     * @return the value of field 'IgnoreGapsinConsensus'.
+     */
+    public boolean getIgnoreGapsinConsensus(
+    ) {
+        return this._ignoreGapsinConsensus;
+    }
 
     /**
      * Returns the value of field 'name'.
      * 
-     * @return String
-     * @return the value of field 'name'.
+     * @return the value of field 'Name'.
      */
-    public java.lang.String getName()
-    {
+    public java.lang.String getName(
+    ) {
         return this._name;
-    } //-- java.lang.String getName() 
+    }
 
     /**
      * Returns the value of field 'outlineColour'.
      * 
-     * @return int
-     * @return the value of field 'outlineColour'.
+     * @return the value of field 'OutlineColour'.
      */
-    public int getOutlineColour()
-    {
+    public int getOutlineColour(
+    ) {
         return this._outlineColour;
-    } //-- int getOutlineColour() 
+    }
 
     /**
      * 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() 
+    }
 
     /**
-     * Method getSeq
-     * 
-     * 
+     * Method getSeq.
      * 
      * @param index
-     * @return int
-     */
-    public int getSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the java.lang.String at the given index
+     */
+    public java.lang.String getSeq(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._seqList.size()) {
+            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
         }
         
-        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-    } //-- int getSeq(int) 
+        return (java.lang.String) _seqList.get(index);
+    }
 
     /**
-     * Method getSeq
-     * 
+     * Method getSeq.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 this collection as an Array
+     */
+    public java.lang.String[] getSeq(
+    ) {
+        java.lang.String[] array = new java.lang.String[0];
+        return (java.lang.String[]) this._seqList.toArray(array);
+    }
+
+    /**
+     * Method getSeqCount.
      * 
-     * @return int
+     * @return the size of this collection
      */
-    public int[] getSeq()
-    {
-        int size = _seqList.size();
-        int[] mArray = new int[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-        }
-        return mArray;
-    } //-- int[] getSeq() 
+    public int getSeqCount(
+    ) {
+        return this._seqList.size();
+    }
 
     /**
-     * Method getSeqCount
+     * Returns the value of field 'showConsensusHistogram'.
      * 
+     * @return the value of field 'ShowConsensusHistogram'.
+     */
+    public boolean getShowConsensusHistogram(
+    ) {
+        return this._showConsensusHistogram;
+    }
+
+    /**
+     * Returns the value of field 'showSequenceLogo'.
      * 
+     * @return the value of field 'ShowSequenceLogo'.
+     */
+    public boolean getShowSequenceLogo(
+    ) {
+        return this._showSequenceLogo;
+    }
+
+    /**
+     * Returns the value of field 'showUnconserved'.
      * 
-     * @return int
+     * @return the value of field 'ShowUnconserved'.
      */
-    public int getSeqCount()
-    {
-        return _seqList.size();
-    } //-- int getSeqCount() 
+    public boolean getShowUnconserved(
+    ) {
+        return this._showUnconserved;
+    }
 
     /**
      * Returns the value of field 'start'.
      * 
-     * @return int
-     * @return the value of field 'start'.
+     * @return the value of field 'Start'.
      */
-    public int getStart()
-    {
+    public int getStart(
+    ) {
         return this._start;
-    } //-- int getStart() 
+    }
 
     /**
      * 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() 
+    }
 
     /**
-     * Method hasColourText
-     * 
+     * Method hasColourText.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one ColourText has been added
      */
-    public boolean hasColourText()
-    {
+    public boolean hasColourText(
+    ) {
         return this._has_colourText;
-    } //-- boolean hasColourText() 
+    }
 
     /**
-     * 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 hasDisplayBoxes
-     * 
-     * 
+     * Method hasDisplayBoxes.
      * 
-     * @return boolean
+     * @return true if at least one DisplayBoxes has been added
      */
-    public boolean hasDisplayBoxes()
-    {
+    public boolean hasDisplayBoxes(
+    ) {
         return this._has_displayBoxes;
-    } //-- boolean hasDisplayBoxes() 
+    }
 
     /**
-     * Method hasDisplayText
+     * Method hasDisplayText.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one DisplayText has been added
      */
-    public boolean hasDisplayText()
-    {
+    public boolean hasDisplayText(
+    ) {
         return this._has_displayText;
-    } //-- boolean hasDisplayText() 
+    }
 
     /**
-     * Method hasEnd
-     * 
+     * Method hasEnd.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one End has been added
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd(
+    ) {
         return this._has_end;
-    } //-- boolean hasEnd() 
+    }
 
     /**
-     * Method hasOutlineColour
-     * 
+     * Method hasIgnoreGapsinConsensus.
      * 
+     * @return true if at least one IgnoreGapsinConsensus has been
+     * added
+     */
+    public boolean hasIgnoreGapsinConsensus(
+    ) {
+        return this._has_ignoreGapsinConsensus;
+    }
+
+    /**
+     * Method hasOutlineColour.
      * 
-     * @return boolean
+     * @return true if at least one OutlineColour has been added
      */
-    public boolean hasOutlineColour()
-    {
+    public boolean hasOutlineColour(
+    ) {
         return this._has_outlineColour;
-    } //-- boolean hasOutlineColour() 
+    }
 
     /**
-     * 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 hasStart
-     * 
+     * Method hasShowConsensusHistogram.
      * 
+     * @return true if at least one ShowConsensusHistogram has been
+     * added
+     */
+    public boolean hasShowConsensusHistogram(
+    ) {
+        return this._has_showConsensusHistogram;
+    }
+
+    /**
+     * Method hasShowSequenceLogo.
      * 
-     * @return boolean
+     * @return true if at least one ShowSequenceLogo has been added
      */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
+    public boolean hasShowSequenceLogo(
+    ) {
+        return this._has_showSequenceLogo;
+    }
 
     /**
-     * Method hasTextCol1
+     * Method hasShowUnconserved.
      * 
+     * @return true if at least one ShowUnconserved has been added
+     */
+    public boolean hasShowUnconserved(
+    ) {
+        return this._has_showUnconserved;
+    }
+
+    /**
+     * Method hasStart.
      * 
+     * @return true if at least one Start has been added
+     */
+    public boolean hasStart(
+    ) {
+        return this._has_start;
+    }
+
+    /**
+     * 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 true if at least one TextCol2 has been added
+     */
+    public boolean hasTextCol2(
+    ) {
+        return this._has_textCol2;
+    }
+
+    /**
+     * Method hasTextColThreshold.
+     * 
+     * @return true if at least one TextColThreshold has been added
+     */
+    public boolean hasTextColThreshold(
+    ) {
+        return this._has_textColThreshold;
+    }
+
+    /**
+     * Returns the value of field 'colourText'.
      * 
+     * @return the value of field 'ColourText'.
+     */
+    public boolean isColourText(
+    ) {
+        return this._colourText;
+    }
+
+    /**
+     * Returns the value of field 'displayBoxes'.
      * 
-     * @return boolean
+     * @return the value of field 'DisplayBoxes'.
      */
-    public boolean hasTextCol2()
-    {
-        return this._has_textCol2;
-    } //-- boolean hasTextCol2() 
+    public boolean isDisplayBoxes(
+    ) {
+        return this._displayBoxes;
+    }
 
     /**
-     * Method hasTextColThreshold
+     * Returns the value of field 'displayText'.
      * 
+     * @return the value of field 'DisplayText'.
+     */
+    public boolean isDisplayText(
+    ) {
+        return this._displayText;
+    }
+
+    /**
+     * Returns the value of field 'ignoreGapsinConsensus'.
      * 
+     * @return the value of field 'IgnoreGapsinConsensus'.
+     */
+    public boolean isIgnoreGapsinConsensus(
+    ) {
+        return this._ignoreGapsinConsensus;
+    }
+
+    /**
+     * Returns the value of field 'showConsensusHistogram'.
      * 
-     * @return boolean
+     * @return the value of field 'ShowConsensusHistogram'.
      */
-    public boolean hasTextColThreshold()
-    {
-        return this._has_textColThreshold;
-    } //-- boolean hasTextColThreshold() 
+    public boolean isShowConsensusHistogram(
+    ) {
+        return this._showConsensusHistogram;
+    }
 
     /**
-     * Method isValid
+     * Returns the value of field 'showSequenceLogo'.
      * 
+     * @return the value of field 'ShowSequenceLogo'.
+     */
+    public boolean isShowSequenceLogo(
+    ) {
+        return this._showSequenceLogo;
+    }
+
+    /**
+     * 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
-     * 
      * 
      * 
      * @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 removeAllSeq
-     * 
      */
-    public void removeAllSeq()
-    {
-        _seqList.removeAllElements();
-    } //-- void removeAllSeq() 
+    public void removeAllSeq(
+    ) {
+        this._seqList.clear();
+    }
 
     /**
-     * Method removeSeq
-     * 
+     * Method removeSeq.
      * 
+     * @param vSeq
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeSeq(
+            final java.lang.String vSeq) {
+        boolean removed = _seqList.remove(vSeq);
+        return removed;
+    }
+
+    /**
+     * Method removeSeqAt.
      * 
      * @param index
-     * @return int
+     * @return the element removed from the collection
      */
-    public int removeSeq(int index)
-    {
-        java.lang.Object obj = _seqList.elementAt(index);
-        _seqList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeSeq(int) 
+    public java.lang.String removeSeqAt(
+            final int index) {
+        java.lang.Object obj = this._seqList.remove(index);
+        return (java.lang.String) obj;
+    }
 
     /**
      * Sets the value of field 'colour'.
      * 
      * @param colour the value of field 'colour'.
      */
-    public void setColour(java.lang.String colour)
-    {
+    public void setColour(
+            final java.lang.String colour) {
         this._colour = colour;
-    } //-- void setColour(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'colourText'.
      * 
      * @param colourText the value of field 'colourText'.
      */
-    public void setColourText(boolean colourText)
-    {
+    public void setColourText(
+            final boolean colourText) {
         this._colourText = colourText;
         this._has_colourText = true;
-    } //-- void setColourText(boolean) 
+    }
 
     /**
      * Sets the value of field 'consThreshold'.
      * 
      * @param consThreshold the value of field 'consThreshold'.
      */
-    public void setConsThreshold(int consThreshold)
-    {
+    public void setConsThreshold(
+            final int consThreshold) {
         this._consThreshold = consThreshold;
         this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
+    }
 
     /**
      * Sets the value of field 'displayBoxes'.
      * 
      * @param displayBoxes the value of field 'displayBoxes'.
      */
-    public void setDisplayBoxes(boolean displayBoxes)
-    {
+    public void setDisplayBoxes(
+            final boolean displayBoxes) {
         this._displayBoxes = displayBoxes;
         this._has_displayBoxes = true;
-    } //-- void setDisplayBoxes(boolean) 
+    }
 
     /**
      * Sets the value of field 'displayText'.
      * 
      * @param displayText the value of field 'displayText'.
      */
-    public void setDisplayText(boolean displayText)
-    {
+    public void setDisplayText(
+            final boolean displayText) {
         this._displayText = displayText;
         this._has_displayText = true;
-    } //-- void setDisplayText(boolean) 
+    }
 
     /**
      * Sets the value of field 'end'.
      * 
      * @param end the value of field 'end'.
      */
-    public void setEnd(int end)
-    {
+    public void setEnd(
+            final int end) {
         this._end = end;
         this._has_end = true;
-    } //-- void setEnd(int) 
+    }
+
+    /**
+     * Sets the value of field 'id'. The field 'id' has the
+     * following description: Optional sequence group ID (only
+     * needs to be unique for this alignment)
+     *  
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(
+            final java.lang.String id) {
+        this._id = id;
+    }
+
+    /**
+     * Sets the value of field 'ignoreGapsinConsensus'.
+     * 
+     * @param ignoreGapsinConsensus the value of field
+     * 'ignoreGapsinConsensus'.
+     */
+    public void setIgnoreGapsinConsensus(
+            final boolean ignoreGapsinConsensus) {
+        this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+        this._has_ignoreGapsinConsensus = true;
+    }
 
     /**
      * Sets the value of field 'name'.
      * 
      * @param name the value of field 'name'.
      */
-    public void setName(java.lang.String name)
-    {
+    public void setName(
+            final java.lang.String name) {
         this._name = name;
-    } //-- void setName(java.lang.String) 
+    }
 
     /**
      * Sets the value of field 'outlineColour'.
      * 
      * @param outlineColour the value of field 'outlineColour'.
      */
-    public void setOutlineColour(int outlineColour)
-    {
+    public void setOutlineColour(
+            final int outlineColour) {
         this._outlineColour = outlineColour;
         this._has_outlineColour = true;
-    } //-- void setOutlineColour(int) 
+    }
 
     /**
      * Sets the value of field 'pidThreshold'.
      * 
      * @param pidThreshold the value of field 'pidThreshold'.
      */
-    public void setPidThreshold(int pidThreshold)
-    {
+    public void setPidThreshold(
+            final int pidThreshold) {
         this._pidThreshold = pidThreshold;
         this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
+    }
 
     /**
-     * Method setSeq
-     * 
      * 
      * 
      * @param index
      * @param vSeq
-     */
-    public void setSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setSeq(
+            final int index,
+            final java.lang.String vSeq)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._seqList.size()) {
+            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
         }
-        _seqList.setElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void setSeq(int, int) 
+        
+        this._seqList.set(index, vSeq);
+    }
 
     /**
-     * Method setSeq
-     * 
      * 
      * 
-     * @param seqArray
+     * @param vSeqArray
      */
-    public void setSeq(int[] seqArray)
-    {
+    public void setSeq(
+            final java.lang.String[] vSeqArray) {
         //-- copy array
-        _seqList.removeAllElements();
-        for (int i = 0; i < seqArray.length; i++) {
-            _seqList.addElement(new java.lang.Integer(seqArray[i]));
+        _seqList.clear();
+        
+        for (int i = 0; i < vSeqArray.length; i++) {
+                this._seqList.add(vSeqArray[i]);
         }
-    } //-- void setSeq(int) 
+    }
+
+    /**
+     * Sets the value of field 'showConsensusHistogram'.
+     * 
+     * @param showConsensusHistogram the value of field
+     * 'showConsensusHistogram'.
+     */
+    public void setShowConsensusHistogram(
+            final boolean showConsensusHistogram) {
+        this._showConsensusHistogram = showConsensusHistogram;
+        this._has_showConsensusHistogram = true;
+    }
+
+    /**
+     * Sets the value of field 'showSequenceLogo'.
+     * 
+     * @param showSequenceLogo the value of field 'showSequenceLogo'
+     */
+    public void setShowSequenceLogo(
+            final boolean showSequenceLogo) {
+        this._showSequenceLogo = showSequenceLogo;
+        this._has_showSequenceLogo = true;
+    }
+
+    /**
+     * 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 'start'.
      * 
      * @param start the value of field 'start'.
      */
-    public void setStart(int start)
-    {
+    public void setStart(
+            final int start) {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int) 
+    }
 
     /**
      * Sets the value of field 'textCol1'.
      * 
      * @param textCol1 the value of field 'textCol1'.
      */
-    public void setTextCol1(int textCol1)
-    {
+    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) 
+    }
 
     /**
-     * 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.JGroup
+     */
+    public static jalview.schemabinding.version2.JGroup unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
         return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+    }
 
     /**
-     * Method validate
      * 
+     * 
+     * @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() 
+    }
 
 }