X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=0000000000000000000000000000000000000000;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=7c6308eb37b563d034e7fb54b19f0894c1a96bba;hpb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
deleted file mode 100644
index 7c6308e..0000000
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ /dev/null
@@ -1,1097 +0,0 @@
-/*
- * 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 _viewreference.
-   */
-  private boolean _viewreference;
-
-  /**
-   * keeps track of state for field: _viewreference
-   */
-  private boolean _has_viewreference;
-
-  /**
-   * Field _featuresList.
-   */
-  private java.util.Vector _featuresList;
-
-  /**
-   * Field _pdbidsList.
-   */
-  private java.util.Vector _pdbidsList;
-
-  /**
-   * Field _hiddenSequencesList.
-   */
-  private java.util.Vector _hiddenSequencesList;
-
-  /**
-   * Reference to a viewer showing RNA structure for this sequence. Schema
-   * supports one viewer showing multiple annotations for multiple sequences,
-   * though currently only one annotation for one sequence (gapped or trimmed)
-   * is used
-   * 
-   */
-  private java.util.Vector _rnaViewerList;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public JSeq()
-  {
-    super();
-    this._featuresList = new java.util.Vector();
-    this._pdbidsList = new java.util.Vector();
-    this._hiddenSequencesList = new java.util.Vector();
-    this._rnaViewerList = 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);
-  }
-
-  /**
-   * 
-   * 
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._rnaViewerList.addElement(vRnaViewer);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addRnaViewer(final int index,
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._rnaViewerList.add(index, vRnaViewer);
-  }
-
-  /**
-     */
-  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;
-  }
-
-  /**
-     */
-  public void deleteViewreference()
-  {
-    this._has_viewreference = 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();
-  }
-
-  /**
-   * Method enumerateRnaViewer.
-   * 
-   * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
-   *         elements
-   */
-  public java.util.Enumeration enumerateRnaViewer()
-  {
-    return this._rnaViewerList.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();
-  }
-
-  /**
-   * Method getRnaViewer.
-   * 
-   * @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.RnaViewer at the
-   *         given index
-   */
-  public jalview.schemabinding.version2.RnaViewer getRnaViewer(
-          final int index) throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._rnaViewerList.size())
-    {
-      throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
-              + index + "' not in range [0.."
-              + (this._rnaViewerList.size() - 1) + "]");
-    }
-
-    return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
-            .get(index);
-  }
-
-  /**
-   * Method getRnaViewer.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.RnaViewer[] getRnaViewer()
-  {
-    jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
-    return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
-            .toArray(array);
-  }
-
-  /**
-   * Method getRnaViewerCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getRnaViewerCount()
-  {
-    return this._rnaViewerList.size();
-  }
-
-  /**
-   * Returns the value of field 'start'.
-   * 
-   * @return the value of field 'Start'.
-   */
-  public int getStart()
-  {
-    return this._start;
-  }
-
-  /**
-   * Returns the value of field 'viewreference'.
-   * 
-   * @return the value of field 'Viewreference'.
-   */
-  public boolean getViewreference()
-  {
-    return this._viewreference;
-  }
-
-  /**
-   * 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;
-  }
-
-  /**
-   * Method hasViewreference.
-   * 
-   * @return true if at least one Viewreference has been added
-   */
-  public boolean hasViewreference()
-  {
-    return this._has_viewreference;
-  }
-
-  /**
-   * 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;
-  }
-
-  /**
-   * Returns the value of field 'viewreference'.
-   * 
-   * @return the value of field 'Viewreference'.
-   */
-  public boolean isViewreference()
-  {
-    return this._viewreference;
-  }
-
-  /**
-   * 
-   * 
-   * @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();
-  }
-
-  /**
-     */
-  public void removeAllRnaViewer()
-  {
-    this._rnaViewerList.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;
-  }
-
-  /**
-   * Method removeRnaViewer.
-   * 
-   * @param vRnaViewer
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-  {
-    boolean removed = _rnaViewerList.remove(vRnaViewer);
-    return removed;
-  }
-
-  /**
-   * Method removeRnaViewerAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
-          final int index)
-  {
-    java.lang.Object obj = this._rnaViewerList.remove(index);
-    return (jalview.schemabinding.version2.RnaViewer) 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]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setRnaViewer(final int index,
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._rnaViewerList.size())
-    {
-      throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
-              + index + "' not in range [0.."
-              + (this._rnaViewerList.size() - 1) + "]");
-    }
-
-    this._rnaViewerList.set(index, vRnaViewer);
-  }
-
-  /**
-   * 
-   * 
-   * @param vRnaViewerArray
-   */
-  public void setRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
-  {
-    // -- copy array
-    _rnaViewerList.clear();
-
-    for (int i = 0; i < vRnaViewerArray.length; i++)
-    {
-      this._rnaViewerList.add(vRnaViewerArray[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;
-  }
-
-  /**
-   * Sets the value of field 'viewreference'.
-   * 
-   * @param viewreference
-   *          the value of field 'viewreference'.
-   */
-  public void setViewreference(final boolean viewreference)
-  {
-    this._viewreference = viewreference;
-    this._has_viewreference = 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);
-  }
-
-}