X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=cad210aa9b919ebbedbc8c6de92758f4d43bcd6a;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0d8dc087db944741f15ec6861df01a5bae3e6700;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 0d8dc08..cad210a 100755
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,637 +1,875 @@
 /*
- * 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 -/
+//---------------------------------/
+//- 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 JSeq.
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _colour
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _start
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _id
-     */
-    private int _id;
-
-    /**
-     * keeps track of state for field: _id
-     */
-    private boolean _has_id;
-
-    /**
-     * Field _featuresList
-     */
-    private java.util.Vector _featuresList;
-
-    /**
-     * Field _pdbidsList
-     */
-    private java.util.Vector _pdbidsList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeq() {
-        super();
-        _featuresList = new Vector();
-        _pdbidsList = new Vector();
-    } //-- jalview.schemabinding.version2.JSeq()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addFeatures
-     * 
-     * 
-     * 
-     * @param vFeatures
-     */
-    public void addFeatures(jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.addElement(vFeatures);
-    } //-- void addFeatures(jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method addFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     */
-    public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.insertElementAt(vFeatures, index);
-    } //-- void addFeatures(int, jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method addPdbids
-     * 
-     * 
-     * 
-     * @param vPdbids
-     */
-    public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.addElement(vPdbids);
-    } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method addPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     */
-    public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.insertElementAt(vPdbids, index);
-    } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method deleteColour
-     * 
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteId
-     * 
-     */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart() 
-
-    /**
-     * Method enumerateFeatures
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateFeatures()
-    {
-        return _featuresList.elements();
-    } //-- java.util.Enumeration enumerateFeatures() 
-
-    /**
-     * Method enumeratePdbids
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumeratePdbids()
-    {
-        return _pdbidsList.elements();
-    } //-- java.util.Enumeration enumeratePdbids() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return int
-     * @return the value of field 'colour'.
-     */
-    public int getColour()
-    {
-        return this._colour;
-    } //-- int getColour() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Method getFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features getFeatures(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Features getFeatures(int) 
-
-    /**
-     * Method getFeatures
-     * 
-     * 
-     * 
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features[] getFeatures()
-    {
-        int size = _featuresList.size();
-        jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Features[] getFeatures() 
-
-    /**
-     * Method getFeaturesCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getFeaturesCount()
-    {
-        return _featuresList.size();
-    } //-- int getFeaturesCount() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return int
-     * @return the value of field 'id'.
-     */
-    public int getId()
-    {
-        return this._id;
-    } //-- int getId() 
-
-    /**
-     * Method getPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids getPdbids(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) 
-
-    /**
-     * Method getPdbids
-     * 
-     * 
-     * 
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids[] getPdbids()
-    {
-        int size = _pdbidsList.size();
-        jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() 
-
-    /**
-     * Method getPdbidsCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getPdbidsCount()
-    {
-        return _pdbidsList.size();
-    } //-- int getPdbidsCount() 
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return int
-     * @return the value of field 'start'.
-     */
-    public int getStart()
-    {
-        return this._start;
-    } //-- int getStart() 
-
-    /**
-     * Method hasColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColour()
-    {
-        return this._has_colour;
-    } //-- boolean hasColour() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasId
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasId()
-    {
-        return this._has_id;
-    } //-- boolean hasId() 
-
-    /**
-     * Method hasStart
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllFeatures
-     * 
-     */
-    public void removeAllFeatures()
-    {
-        _featuresList.removeAllElements();
-    } //-- void removeAllFeatures() 
-
-    /**
-     * Method removeAllPdbids
-     * 
-     */
-    public void removeAllPdbids()
-    {
-        _pdbidsList.removeAllElements();
-    } //-- void removeAllPdbids() 
-
-    /**
-     * Method removeFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features removeFeatures(int index)
-    {
-        java.lang.Object obj = _featuresList.elementAt(index);
-        _featuresList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Features) obj;
-    } //-- jalview.schemabinding.version2.Features removeFeatures(int) 
-
-    /**
-     * Method removePdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids removePdbids(int index)
-    {
-        java.lang.Object obj = _pdbidsList.elementAt(index);
-        _pdbidsList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Pdbids) obj;
-    } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(int colour)
-    {
-        this._colour = colour;
-        this._has_colour = true;
-    } //-- void setColour(int) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Method setFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     */
-    public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _featuresList.setElementAt(vFeatures, index);
-    } //-- void setFeatures(int, jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method setFeatures
-     * 
-     * 
-     * 
-     * @param featuresArray
-     */
-    public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)
-    {
-        //-- copy array
-        _featuresList.removeAllElements();
-        for (int i = 0; i < featuresArray.length; i++) {
-            _featuresList.addElement(featuresArray[i]);
-        }
-    } //-- void setFeatures(jalview.schemabinding.version2.Features) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(int id)
-    {
-        this._id = id;
-        this._has_id = true;
-    } //-- void setId(int) 
-
-    /**
-     * Method setPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     */
-    public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _pdbidsList.setElementAt(vPdbids, index);
-    } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method setPdbids
-     * 
-     * 
-     * 
-     * @param pdbidsArray
-     */
-    public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)
-    {
-        //-- copy array
-        _pdbidsList.removeAllElements();
-        for (int i = 0; i < pdbidsArray.length; i++) {
-            _pdbidsList.addElement(pdbidsArray[i]);
-        }
-    } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(int start)
-    {
-        this._start = start;
-        this._has_start = true;
-    } //-- void setStart(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+public class JSeq implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _hidden.
+   */
+  private boolean _hidden;
+
+  /**
+   * keeps track of state for field: _hidden
+   */
+  private boolean _has_hidden;
+
+  /**
+   * Field _featuresList.
+   */
+  private java.util.Vector _featuresList;
+
+  /**
+   * Field _pdbidsList.
+   */
+  private java.util.Vector _pdbidsList;
+
+  /**
+   * Field _hiddenSequencesList.
+   */
+  private java.util.Vector _hiddenSequencesList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeq()
+  {
+    super();
+    this._featuresList = new java.util.Vector();
+    this._pdbidsList = new java.util.Vector();
+    this._hiddenSequencesList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.addElement(vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.add(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.addElement(new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.add(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.addElement(vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.add(index, vPdbids);
+  }
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteHidden()
+  {
+    this._has_hidden = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateFeatures.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Features
+   *         elements
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return this._featuresList.elements();
+  }
+
+  /**
+   * Method enumerateHiddenSequences.
+   * 
+   * @return an Enumeration over all int elements
+   */
+  public java.util.Enumeration enumerateHiddenSequences()
+  {
+    return this._hiddenSequencesList.elements();
+  }
+
+  /**
+   * Method enumeratePdbids.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
+   *         elements
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return this._pdbidsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Method getFeatures.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Features at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Features getFeatures(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("getFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Features) _featuresList
+            .get(index);
+  }
+
+  /**
+   * Method getFeatures.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 jalview.schemabinding.version2.Features[] getFeatures()
+  {
+    jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+    return (jalview.schemabinding.version2.Features[]) this._featuresList
+            .toArray(array);
+  }
+
+  /**
+   * Method getFeaturesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFeaturesCount()
+  {
+    return this._featuresList.size();
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean getHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * Method getHiddenSequences.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the int at the given index
+   */
+  public int getHiddenSequences(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+  }
+
+  /**
+   * Method getHiddenSequences.Returns the contents of the collection in an
+   * Array.
+   * 
+   * @return this collection as an Array
+   */
+  public int[] getHiddenSequences()
+  {
+    int size = this._hiddenSequencesList.size();
+    int[] array = new int[size];
+    java.util.Iterator iter = _hiddenSequencesList.iterator();
+    for (int index = 0; index < size; index++)
+    {
+      array[index] = ((java.lang.Integer) iter.next()).intValue();
+    }
+    return array;
+  }
+
+  /**
+   * Method getHiddenSequencesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getHiddenSequencesCount()
+  {
+    return this._hiddenSequencesList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbids.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Pdbids at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+  }
+
+  /**
+   * Method getPdbids.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 jalview.schemabinding.version2.Pdbids[] getPdbids()
+  {
+    jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+    return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPdbidsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbidsCount()
+  {
+    return this._pdbidsList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasHidden.
+   * 
+   * @return true if at least one Hidden has been added
+   */
+  public boolean hasHidden()
+  {
+    return this._has_hidden;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean isHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * 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)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @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(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @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);
+  }
+
+  /**
+     */
+  public void removeAllFeatures()
+  {
+    this._featuresList.clear();
+  }
+
+  /**
+     */
+  public void removeAllHiddenSequences()
+  {
+    this._hiddenSequencesList.clear();
+  }
+
+  /**
+     */
+  public void removeAllPdbids()
+  {
+    this._pdbidsList.clear();
+  }
+
+  /**
+   * Method removeFeatures.
+   * 
+   * @param vFeatures
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+  {
+    boolean removed = _featuresList.remove(vFeatures);
+    return removed;
+  }
+
+  /**
+   * Method removeFeaturesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Features removeFeaturesAt(
+          final int index)
+  {
+    java.lang.Object obj = this._featuresList.remove(index);
+    return (jalview.schemabinding.version2.Features) obj;
+  }
+
+  /**
+   * Method removeHiddenSequences.
+   * 
+   * @param vHiddenSequences
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeHiddenSequences(final int vHiddenSequences)
+  {
+    boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
+            vHiddenSequences));
+    return removed;
+  }
+
+  /**
+   * Method removeHiddenSequencesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public int removeHiddenSequencesAt(final int index)
+  {
+    java.lang.Object obj = this._hiddenSequencesList.remove(index);
+    return ((java.lang.Integer) obj).intValue();
+  }
+
+  /**
+   * Method removePdbids.
+   * 
+   * @param vPdbids
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbids(
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+  {
+    boolean removed = _pdbidsList.remove(vPdbids);
+    return removed;
+  }
+
+  /**
+   * Method removePdbidsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+          final int index)
+  {
+    java.lang.Object obj = this._pdbidsList.remove(index);
+    return (jalview.schemabinding.version2.Pdbids) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("setFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    this._featuresList.set(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFeaturesArray
+   */
+  public void setFeatures(
+          final jalview.schemabinding.version2.Features[] vFeaturesArray)
+  {
+    // -- copy array
+    _featuresList.clear();
+
+    for (int i = 0; i < vFeaturesArray.length; i++)
+    {
+      this._featuresList.add(vFeaturesArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'hidden'.
+   * 
+   * @param hidden
+   *          the value of field 'hidden'.
+   */
+  public void setHidden(final boolean hidden)
+  {
+    this._hidden = hidden;
+    this._has_hidden = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    this._hiddenSequencesList.set(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequencesArray
+   */
+  public void setHiddenSequences(final int[] vHiddenSequencesArray)
+  {
+    // -- copy array
+    _hiddenSequencesList.clear();
+
+    for (int i = 0; i < vHiddenSequencesArray.length; i++)
+    {
+      this._hiddenSequencesList.add(new java.lang.Integer(
+              vHiddenSequencesArray[i]));
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    this._pdbidsList.set(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbidsArray
+   */
+  public void setPdbids(
+          final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
+  {
+    // -- copy array
+    _pdbidsList.clear();
+
+    for (int i = 0; i < vPdbidsArray.length; i++)
+    {
+      this._pdbidsList.add(vPdbidsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @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.JSeq
+   */
+  public static jalview.schemabinding.version2.JSeq unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.JSeq.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @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
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }