X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=d6d019285da41614303df742067865b0d8c65509;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=29221ad2963b2444dbd260100490b9f5d8d06097;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
old mode 100755
new mode 100644
index 29221ad..d6d0192
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,867 +1,831 @@
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
-
-import org.exolab.castor.xml.*;
-
-/**
- * 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 _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();
-    _featuresList = new Vector();
-    _pdbidsList = new Vector();
-    _hiddenSequencesList = 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 addHiddenSequences
-   *
-   *
-   *
-   * @param vHiddenSequences
-   */
-  public void addHiddenSequences(int vHiddenSequences)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
-  } //-- void addHiddenSequences(int)
-
-  /**
-   * Method addHiddenSequences
-   *
-   *
-   *
-   * @param index
-   * @param vHiddenSequences
-   */
-  public void addHiddenSequences(int index, int vHiddenSequences)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences),
-                                         index);
-  } //-- void addHiddenSequences(int, int)
-
-  /**
-   * 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 deleteHidden
-   *
-   */
-  public void deleteHidden()
-  {
-    this._has_hidden = false;
-  } //-- void deleteHidden()
-
-  /**
-   * 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 enumerateHiddenSequences
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateHiddenSequences()
-  {
-    return _hiddenSequencesList.elements();
-  } //-- java.util.Enumeration enumerateHiddenSequences()
-
-  /**
-   * 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 'hidden'.
-   *
-   * @return boolean
-   * @return the value of field 'hidden'.
-   */
-  public boolean getHidden()
-  {
-    return this._hidden;
-  } //-- boolean getHidden()
-
-  /**
-   * Method getHiddenSequences
-   *
-   *
-   *
-   * @param index
-   * @return int
-   */
-  public int getHiddenSequences(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _hiddenSequencesList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return ( (java.lang.Integer) _hiddenSequencesList.elementAt(index)).
-        intValue();
-  } //-- int getHiddenSequences(int)
-
-  /**
-   * Method getHiddenSequences
-   *
-   *
-   *
-   * @return int
-   */
-  public int[] getHiddenSequences()
-  {
-    int size = _hiddenSequencesList.size();
-    int[] mArray = new int[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = ( (java.lang.Integer) _hiddenSequencesList.elementAt(
-          index)).intValue();
-    }
-    return mArray;
-  } //-- int[] getHiddenSequences()
-
-  /**
-   * Method getHiddenSequencesCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getHiddenSequencesCount()
-  {
-    return _hiddenSequencesList.size();
-  } //-- int getHiddenSequencesCount()
-
-  /**
-   * 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 hasHidden
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasHidden()
-  {
-    return this._has_hidden;
-  } //-- boolean hasHidden()
-
-  /**
-   * 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 removeAllHiddenSequences
-   *
-   */
-  public void removeAllHiddenSequences()
-  {
-    _hiddenSequencesList.removeAllElements();
-  } //-- void removeAllHiddenSequences()
-
-  /**
-   * 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 removeHiddenSequences
-   *
-   *
-   *
-   * @param index
-   * @return int
-   */
-  public int removeHiddenSequences(int index)
-  {
-    java.lang.Object obj = _hiddenSequencesList.elementAt(index);
-    _hiddenSequencesList.removeElementAt(index);
-    return ( (java.lang.Integer) obj).intValue();
-  } //-- int removeHiddenSequences(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 'hidden'.
-   *
-   * @param hidden the value of field 'hidden'.
-   */
-  public void setHidden(boolean hidden)
-  {
-    this._hidden = hidden;
-    this._has_hidden = true;
-  } //-- void setHidden(boolean)
-
-  /**
-   * Method setHiddenSequences
-   *
-   *
-   *
-   * @param index
-   * @param vHiddenSequences
-   */
-  public void setHiddenSequences(int index, int vHiddenSequences)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _hiddenSequencesList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences),
-                                      index);
-  } //-- void setHiddenSequences(int, int)
-
-  /**
-   * Method setHiddenSequences
-   *
-   *
-   *
-   * @param hiddenSequencesArray
-   */
-  public void setHiddenSequences(int[] hiddenSequencesArray)
-  {
-    //-- copy array
-    _hiddenSequencesList.removeAllElements();
-    for (int i = 0; i < hiddenSequencesArray.length; i++)
-    {
-      _hiddenSequencesList.addElement(new java.lang.Integer(
-          hiddenSequencesArray[i]));
-    }
-  } //-- void setHiddenSequences(int)
-
-  /**
-   * 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()
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * 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 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);
+    }
+
+}