X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=4da0f75f76ed3f64cf6def9c2327192bd10cf919;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=49edb8df01d66cbe9e42809152abb8adcdfb7fff;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 49edb8d..4da0f75 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,35 +1,43 @@
 /*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.schemabinding.version2;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import java.util.*;
-
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class JGroup.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class JGroup
-    implements java.io.Serializable
+public class JGroup implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _start
+   * Field _start.
    */
   private int _start;
 
@@ -39,7 +47,7 @@ public class JGroup
   private boolean _has_start;
 
   /**
-   * Field _end
+   * Field _end.
    */
   private int _end;
 
@@ -49,17 +57,17 @@ public class JGroup
   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;
 
@@ -69,7 +77,7 @@ public class JGroup
   private boolean _has_consThreshold;
 
   /**
-   * Field _pidThreshold
+   * Field _pidThreshold.
    */
   private int _pidThreshold;
 
@@ -79,7 +87,7 @@ public class JGroup
   private boolean _has_pidThreshold;
 
   /**
-   * Field _outlineColour
+   * Field _outlineColour.
    */
   private int _outlineColour;
 
@@ -89,7 +97,7 @@ public class JGroup
   private boolean _has_outlineColour;
 
   /**
-   * Field _displayBoxes
+   * Field _displayBoxes.
    */
   private boolean _displayBoxes;
 
@@ -99,7 +107,7 @@ public class JGroup
   private boolean _has_displayBoxes;
 
   /**
-   * Field _displayText
+   * Field _displayText.
    */
   private boolean _displayText;
 
@@ -109,7 +117,7 @@ public class JGroup
   private boolean _has_displayText;
 
   /**
-   * Field _colourText
+   * Field _colourText.
    */
   private boolean _colourText;
 
@@ -119,7 +127,7 @@ public class JGroup
   private boolean _has_colourText;
 
   /**
-   * Field _textCol1
+   * Field _textCol1.
    */
   private int _textCol1;
 
@@ -129,7 +137,7 @@ public class JGroup
   private boolean _has_textCol1;
 
   /**
-   * Field _textCol2
+   * Field _textCol2.
    */
   private int _textCol2;
 
@@ -139,7 +147,7 @@ public class JGroup
   private boolean _has_textCol2;
 
   /**
-   * Field _textColThreshold
+   * Field _textColThreshold.
    */
   private int _textColThreshold;
 
@@ -149,764 +157,1028 @@ public class JGroup
   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;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public JGroup()
   {
     super();
-    _seqList = new Vector();
-  } //-- jalview.schemabinding.version2.JGroup()
+    this._seqList = new java.util.Vector();
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
   /**
-   * 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
+  public void addSeq(final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _seqList.addElement(new java.lang.Integer(vSeq));
-  } //-- void addSeq(int)
+    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
+  public void addSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-  } //-- void addSeq(int, int)
+    this._seqList.add(index, vSeq);
+  }
 
   /**
-   * Method deleteColourText
-   *
-   */
+     */
   public void deleteColourText()
   {
     this._has_colourText = false;
-  } //-- void deleteColourText()
+  }
 
   /**
-   * Method deleteConsThreshold
-   *
-   */
+     */
   public void deleteConsThreshold()
   {
     this._has_consThreshold = false;
-  } //-- void deleteConsThreshold()
+  }
 
   /**
-   * Method deleteDisplayBoxes
-   *
-   */
+     */
   public void deleteDisplayBoxes()
   {
     this._has_displayBoxes = false;
-  } //-- void deleteDisplayBoxes()
+  }
 
   /**
-   * Method deleteDisplayText
-   *
-   */
+     */
   public void deleteDisplayText()
   {
     this._has_displayText = false;
-  } //-- void deleteDisplayText()
+  }
 
   /**
-   * Method deleteEnd
-   *
-   */
+     */
   public void deleteEnd()
   {
     this._has_end = false;
-  } //-- void deleteEnd()
+  }
 
   /**
-   * Method deleteOutlineColour
-   *
-   */
+     */
+  public void deleteIgnoreGapsinConsensus()
+  {
+    this._has_ignoreGapsinConsensus = false;
+  }
+
+  /**
+     */
   public void deleteOutlineColour()
   {
     this._has_outlineColour = false;
-  } //-- void deleteOutlineColour()
+  }
 
   /**
-   * Method deletePidThreshold
-   *
-   */
+     */
   public void deletePidThreshold()
   {
     this._has_pidThreshold = false;
-  } //-- void deletePidThreshold()
+  }
 
   /**
-   * Method 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()
   {
     this._has_textCol1 = false;
-  } //-- void deleteTextCol1()
+  }
 
   /**
-   * Method deleteTextCol2
-   *
-   */
+     */
   public void deleteTextCol2()
   {
     this._has_textCol2 = false;
-  } //-- void deleteTextCol2()
+  }
 
   /**
-   * Method deleteTextColThreshold
-   *
-   */
+     */
   public void deleteTextColThreshold()
   {
     this._has_textColThreshold = false;
-  } //-- void deleteTextColThreshold()
+  }
 
   /**
-   * Method enumerateSeq
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateSeq.
+   * 
+   * @return an Enumeration over all java.lang.String elements
    */
   public java.util.Enumeration enumerateSeq()
   {
-    return _seqList.elements();
-  } //-- 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()
   {
     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()
   {
     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()
   {
     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()
   {
     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()
   {
     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()
   {
     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()
   {
     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()
   {
     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()
   {
     return this._pidThreshold;
-  } //-- int getPidThreshold()
+  }
 
   /**
-   * Method getSeq
-   *
-   *
-   *
+   * Method getSeq.
+   * 
    * @param index
-   * @return int
+   * @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 int getSeq(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public java.lang.String getSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _seqList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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
-   *
-   *
-   *
-   * @return int
+   * 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 int[] getSeq()
+  public java.lang.String[] 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()
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._seqList.toArray(array);
+  }
 
   /**
-   * Method getSeqCount
-   *
-   *
-   *
-   * @return int
+   * Method getSeqCount.
+   * 
+   * @return the size of this collection
    */
   public int getSeqCount()
   {
-    return _seqList.size();
-  } //-- int getSeqCount()
+    return this._seqList.size();
+  }
+
+  /**
+   * 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 the value of field 'ShowUnconserved'.
+   */
+  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()
   {
     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()
   {
     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()
   {
     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()
   {
     return this._textColThreshold;
-  } //-- int getTextColThreshold()
+  }
 
   /**
-   * Method hasColourText
-   *
-   *
-   *
-   * @return boolean
+   * Method hasColourText.
+   * 
+   * @return true if at least one ColourText has been added
    */
   public boolean hasColourText()
   {
     return this._has_colourText;
-  } //-- boolean hasColourText()
+  }
 
   /**
-   * Method hasConsThreshold
-   *
-   *
-   *
-   * @return boolean
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
    */
   public boolean hasConsThreshold()
   {
     return this._has_consThreshold;
-  } //-- boolean hasConsThreshold()
+  }
 
   /**
-   * Method hasDisplayBoxes
-   *
-   *
-   *
-   * @return boolean
+   * Method hasDisplayBoxes.
+   * 
+   * @return true if at least one DisplayBoxes has been added
    */
   public boolean hasDisplayBoxes()
   {
     return this._has_displayBoxes;
-  } //-- boolean hasDisplayBoxes()
+  }
 
   /**
-   * Method hasDisplayText
-   *
-   *
-   *
-   * @return boolean
+   * Method hasDisplayText.
+   * 
+   * @return true if at least one DisplayText has been added
    */
   public boolean hasDisplayText()
   {
     return this._has_displayText;
-  } //-- boolean hasDisplayText()
+  }
 
   /**
-   * Method hasEnd
-   *
-   *
-   *
-   * @return boolean
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
    */
   public boolean hasEnd()
   {
     return this._has_end;
-  } //-- boolean hasEnd()
+  }
 
   /**
-   * Method hasOutlineColour
-   *
-   *
-   *
-   * @return boolean
+   * Method hasIgnoreGapsinConsensus.
+   * 
+   * @return true if at least one IgnoreGapsinConsensus has been added
+   */
+  public boolean hasIgnoreGapsinConsensus()
+  {
+    return this._has_ignoreGapsinConsensus;
+  }
+
+  /**
+   * Method hasOutlineColour.
+   * 
+   * @return true if at least one OutlineColour has been added
    */
   public boolean hasOutlineColour()
   {
     return this._has_outlineColour;
-  } //-- boolean hasOutlineColour()
+  }
 
   /**
-   * Method hasPidThreshold
-   *
-   *
-   *
-   * @return boolean
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
    */
   public boolean hasPidThreshold()
   {
     return this._has_pidThreshold;
-  } //-- boolean hasPidThreshold()
+  }
 
   /**
-   * Method hasStart
-   *
-   *
-   *
-   * @return boolean
+   * Method hasShowConsensusHistogram.
+   * 
+   * @return true if at least one ShowConsensusHistogram has been added
+   */
+  public boolean hasShowConsensusHistogram()
+  {
+    return this._has_showConsensusHistogram;
+  }
+
+  /**
+   * Method hasShowSequenceLogo.
+   * 
+   * @return true if at least one ShowSequenceLogo has been added
+   */
+  public boolean hasShowSequenceLogo()
+  {
+    return this._has_showSequenceLogo;
+  }
+
+  /**
+   * 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;
-  } //-- boolean hasStart()
+  }
 
   /**
-   * Method hasTextCol1
-   *
-   *
-   *
-   * @return boolean
+   * Method hasTextCol1.
+   * 
+   * @return true if at least one TextCol1 has been added
    */
   public boolean hasTextCol1()
   {
     return this._has_textCol1;
-  } //-- boolean hasTextCol1()
+  }
 
   /**
-   * Method hasTextCol2
-   *
-   *
-   *
-   * @return boolean
+   * Method hasTextCol2.
+   * 
+   * @return true if at least one TextCol2 has been added
    */
   public boolean hasTextCol2()
   {
     return this._has_textCol2;
-  } //-- boolean hasTextCol2()
+  }
 
   /**
-   * Method hasTextColThreshold
-   *
-   *
-   *
-   * @return boolean
+   * Method hasTextColThreshold.
+   * 
+   * @return true if at least one TextColThreshold has been added
    */
   public boolean hasTextColThreshold()
   {
     return this._has_textColThreshold;
-  } //-- boolean hasTextColThreshold()
+  }
+
+  /**
+   * 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 the value of field 'DisplayBoxes'.
+   */
+  public boolean isDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * 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 the value of field 'ShowConsensusHistogram'.
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return this._showConsensusHistogram;
+  }
+
+  /**
+   * 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
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
    */
   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
+   * @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(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  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()
+    this._seqList.clear();
+  }
+
+  /**
+   * 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 removeSeq
-   *
-   *
-   *
+   * Method removeSeqAt.
+   * 
    * @param index
-   * @return int
+   * @return the element removed from the collection
    */
-  public int removeSeq(int index)
+  public java.lang.String removeSeqAt(final int index)
   {
-    java.lang.Object obj = _seqList.elementAt(index);
-    _seqList.removeElementAt(index);
-    return ( (java.lang.Integer) obj).intValue();
-  } //-- int removeSeq(int)
+    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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void setSeq(int index, int vSeq)
-      throws java.lang.IndexOutOfBoundsException
+  public void setSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _seqList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
     {
-      throw new IndexOutOfBoundsException();
+      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++)
+    // -- copy array
+    _seqList.clear();
+
+    for (int i = 0; i < vSeqArray.length; i++)
     {
-      _seqList.addElement(new java.lang.Integer(seqArray[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'.
+   * 
+   * @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'.
+   * 
+   * @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'.
+   * 
+   * @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'
+   * 
+   * @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)
+            jalview.schemabinding.version2.JGroup.class, 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();
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
     validator.validate(this);
-  } //-- void validate()
+  }
 
 }