/*
 * 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 PcaViewer.
 * 
 * @version $Revision$ $Date$
 */
public class PcaViewer implements java.io.Serializable
{

  // --------------------------/
  // - Class/Member Variables -/
  // --------------------------/

  /**
   * Field _title.
   */
  private java.lang.String _title;

  /**
   * Field _scoreModelName.
   */
  private java.lang.String _scoreModelName;

  /**
   * Field _xDim.
   */
  private int _xDim;

  /**
   * keeps track of state for field: _xDim
   */
  private boolean _has_xDim;

  /**
   * Field _yDim.
   */
  private int _yDim;

  /**
   * keeps track of state for field: _yDim
   */
  private boolean _has_yDim;

  /**
   * Field _zDim.
   */
  private int _zDim;

  /**
   * keeps track of state for field: _zDim
   */
  private boolean _has_zDim;

  /**
   * Field _bgColour.
   */
  private int _bgColour;

  /**
   * keeps track of state for field: _bgColour
   */
  private boolean _has_bgColour;

  /**
   * Field _scaleFactor.
   */
  private float _scaleFactor;

  /**
   * keeps track of state for field: _scaleFactor
   */
  private boolean _has_scaleFactor;

  /**
   * Field _showLabels.
   */
  private boolean _showLabels;

  /**
   * keeps track of state for field: _showLabels
   */
  private boolean _has_showLabels;

  /**
   * Field _linkToAllViews.
   */
  private boolean _linkToAllViews;

  /**
   * keeps track of state for field: _linkToAllViews
   */
  private boolean _has_linkToAllViews;

  /**
   * Field _includeGaps.
   */
  private boolean _includeGaps;

  /**
   * keeps track of state for field: _includeGaps
   */
  private boolean _has_includeGaps;

  /**
   * Field _matchGaps.
   */
  private boolean _matchGaps;

  /**
   * keeps track of state for field: _matchGaps
   */
  private boolean _has_matchGaps;

  /**
   * Field _includeGappedColumns.
   */
  private boolean _includeGappedColumns;

  /**
   * keeps track of state for field: _includeGappedColumns
   */
  private boolean _has_includeGappedColumns;

  /**
   * Field _denominateByShortestLength.
   */
  private boolean _denominateByShortestLength;

  /**
   * keeps track of state for field: _denominateByShortestLength
   */
  private boolean _has_denominateByShortestLength;

  /**
   * Field _width.
   */
  private int _width;

  /**
   * keeps track of state for field: _width
   */
  private boolean _has_width;

  /**
   * Field _height.
   */
  private int _height;

  /**
   * keeps track of state for field: _height
   */
  private boolean _has_height;

  /**
   * Field _xpos.
   */
  private int _xpos;

  /**
   * keeps track of state for field: _xpos
   */
  private boolean _has_xpos;

  /**
   * Field _ypos.
   */
  private int _ypos;

  /**
   * keeps track of state for field: _ypos
   */
  private boolean _has_ypos;

  /**
   * Field _sequencePointList.
   */
  private java.util.Vector _sequencePointList;

  /**
   * endpoints of X, Y and Z axes in that order
   * 
   */
  private java.util.Vector _axisList;

  /**
   * Field _seqPointMin.
   */
  private jalview.schemabinding.version2.SeqPointMin _seqPointMin;

  /**
   * Field _seqPointMax.
   */
  private jalview.schemabinding.version2.SeqPointMax _seqPointMax;

  /**
   * Field _pcaData.
   */
  private jalview.schemabinding.version2.PcaData _pcaData;

  // ----------------/
  // - Constructors -/
  // ----------------/

  public PcaViewer()
  {
    super();
    this._sequencePointList = new java.util.Vector();
    this._axisList = new java.util.Vector();
  }

  // -----------/
  // - Methods -/
  // -----------/

  /**
   * 
   * 
   * @param vAxis
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addAxis(final jalview.schemabinding.version2.Axis vAxis)
          throws java.lang.IndexOutOfBoundsException
  {
    // check for the maximum size
    if (this._axisList.size() >= 3)
    {
      throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
    }

    this._axisList.addElement(vAxis);
  }

  /**
   * 
   * 
   * @param index
   * @param vAxis
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addAxis(final int index,
          final jalview.schemabinding.version2.Axis vAxis)
          throws java.lang.IndexOutOfBoundsException
  {
    // check for the maximum size
    if (this._axisList.size() >= 3)
    {
      throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
    }

    this._axisList.add(index, vAxis);
  }

  /**
   * 
   * 
   * @param vSequencePoint
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addSequencePoint(
          final jalview.schemabinding.version2.SequencePoint vSequencePoint)
          throws java.lang.IndexOutOfBoundsException
  {
    this._sequencePointList.addElement(vSequencePoint);
  }

  /**
   * 
   * 
   * @param index
   * @param vSequencePoint
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addSequencePoint(final int index,
          final jalview.schemabinding.version2.SequencePoint vSequencePoint)
          throws java.lang.IndexOutOfBoundsException
  {
    this._sequencePointList.add(index, vSequencePoint);
  }

  /**
   */
  public void deleteBgColour()
  {
    this._has_bgColour = false;
  }

  /**
   */
  public void deleteDenominateByShortestLength()
  {
    this._has_denominateByShortestLength = false;
  }

  /**
   */
  public void deleteHeight()
  {
    this._has_height = false;
  }

  /**
   */
  public void deleteIncludeGappedColumns()
  {
    this._has_includeGappedColumns = false;
  }

  /**
   */
  public void deleteIncludeGaps()
  {
    this._has_includeGaps = false;
  }

  /**
   */
  public void deleteLinkToAllViews()
  {
    this._has_linkToAllViews = false;
  }

  /**
   */
  public void deleteMatchGaps()
  {
    this._has_matchGaps = false;
  }

  /**
   */
  public void deleteScaleFactor()
  {
    this._has_scaleFactor = false;
  }

  /**
   */
  public void deleteShowLabels()
  {
    this._has_showLabels = false;
  }

  /**
   */
  public void deleteWidth()
  {
    this._has_width = false;
  }

  /**
   */
  public void deleteXDim()
  {
    this._has_xDim = false;
  }

  /**
   */
  public void deleteXpos()
  {
    this._has_xpos = false;
  }

  /**
   */
  public void deleteYDim()
  {
    this._has_yDim = false;
  }

  /**
   */
  public void deleteYpos()
  {
    this._has_ypos = false;
  }

  /**
   */
  public void deleteZDim()
  {
    this._has_zDim = false;
  }

  /**
   * Method enumerateAxis.
   * 
   * @return an Enumeration over all jalview.schemabinding.version2.Axis
   *         elements
   */
  public java.util.Enumeration enumerateAxis()
  {
    return this._axisList.elements();
  }

  /**
   * Method enumerateSequencePoint.
   * 
   * @return an Enumeration over all
   *         jalview.schemabinding.version2.SequencePoint elements
   */
  public java.util.Enumeration enumerateSequencePoint()
  {
    return this._sequencePointList.elements();
  }

  /**
   * Method getAxis.
   * 
   * @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.Axis at the given
   *         index
   */
  public jalview.schemabinding.version2.Axis getAxis(final int index)
          throws java.lang.IndexOutOfBoundsException
  {
    // check bounds for index
    if (index < 0 || index >= this._axisList.size())
    {
      throw new IndexOutOfBoundsException("getAxis: Index value '" + index
              + "' not in range [0.." + (this._axisList.size() - 1) + "]");
    }

    return (jalview.schemabinding.version2.Axis) _axisList.get(index);
  }

  /**
   * Method getAxis.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.Axis[] getAxis()
  {
    jalview.schemabinding.version2.Axis[] array = new jalview.schemabinding.version2.Axis[0];
    return (jalview.schemabinding.version2.Axis[]) this._axisList
            .toArray(array);
  }

  /**
   * Method getAxisCount.
   * 
   * @return the size of this collection
   */
  public int getAxisCount()
  {
    return this._axisList.size();
  }

  /**
   * Returns the value of field 'bgColour'.
   * 
   * @return the value of field 'BgColour'.
   */
  public int getBgColour()
  {
    return this._bgColour;
  }

  /**
   * Returns the value of field 'denominateByShortestLength'.
   * 
   * @return the value of field 'DenominateByShortestLength'.
   */
  public boolean getDenominateByShortestLength()
  {
    return this._denominateByShortestLength;
  }

  /**
   * Returns the value of field 'height'.
   * 
   * @return the value of field 'Height'.
   */
  public int getHeight()
  {
    return this._height;
  }

  /**
   * Returns the value of field 'includeGappedColumns'.
   * 
   * @return the value of field 'IncludeGappedColumns'.
   */
  public boolean getIncludeGappedColumns()
  {
    return this._includeGappedColumns;
  }

  /**
   * Returns the value of field 'includeGaps'.
   * 
   * @return the value of field 'IncludeGaps'.
   */
  public boolean getIncludeGaps()
  {
    return this._includeGaps;
  }

  /**
   * Returns the value of field 'linkToAllViews'.
   * 
   * @return the value of field 'LinkToAllViews'.
   */
  public boolean getLinkToAllViews()
  {
    return this._linkToAllViews;
  }

  /**
   * Returns the value of field 'matchGaps'.
   * 
   * @return the value of field 'MatchGaps'.
   */
  public boolean getMatchGaps()
  {
    return this._matchGaps;
  }

  /**
   * Returns the value of field 'pcaData'.
   * 
   * @return the value of field 'PcaData'.
   */
  public jalview.schemabinding.version2.PcaData getPcaData()
  {
    return this._pcaData;
  }

  /**
   * Returns the value of field 'scaleFactor'.
   * 
   * @return the value of field 'ScaleFactor'.
   */
  public float getScaleFactor()
  {
    return this._scaleFactor;
  }

  /**
   * Returns the value of field 'scoreModelName'.
   * 
   * @return the value of field 'ScoreModelName'.
   */
  public java.lang.String getScoreModelName()
  {
    return this._scoreModelName;
  }

  /**
   * Returns the value of field 'seqPointMax'.
   * 
   * @return the value of field 'SeqPointMax'.
   */
  public jalview.schemabinding.version2.SeqPointMax getSeqPointMax()
  {
    return this._seqPointMax;
  }

  /**
   * Returns the value of field 'seqPointMin'.
   * 
   * @return the value of field 'SeqPointMin'.
   */
  public jalview.schemabinding.version2.SeqPointMin getSeqPointMin()
  {
    return this._seqPointMin;
  }

  /**
   * Method getSequencePoint.
   * 
   * @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.SequencePoint at
   *         the given index
   */
  public jalview.schemabinding.version2.SequencePoint getSequencePoint(
          final int index) throws java.lang.IndexOutOfBoundsException
  {
    // check bounds for index
    if (index < 0 || index >= this._sequencePointList.size())
    {
      throw new IndexOutOfBoundsException("getSequencePoint: Index value '"
              + index + "' not in range [0.."
              + (this._sequencePointList.size() - 1) + "]");
    }

    return (jalview.schemabinding.version2.SequencePoint) _sequencePointList
            .get(index);
  }

  /**
   * Method getSequencePoint.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.SequencePoint[] getSequencePoint()
  {
    jalview.schemabinding.version2.SequencePoint[] array = new jalview.schemabinding.version2.SequencePoint[0];
    return (jalview.schemabinding.version2.SequencePoint[]) this._sequencePointList
            .toArray(array);
  }

  /**
   * Method getSequencePointCount.
   * 
   * @return the size of this collection
   */
  public int getSequencePointCount()
  {
    return this._sequencePointList.size();
  }

  /**
   * Returns the value of field 'showLabels'.
   * 
   * @return the value of field 'ShowLabels'.
   */
  public boolean getShowLabels()
  {
    return this._showLabels;
  }

  /**
   * Returns the value of field 'title'.
   * 
   * @return the value of field 'Title'.
   */
  public java.lang.String getTitle()
  {
    return this._title;
  }

  /**
   * Returns the value of field 'width'.
   * 
   * @return the value of field 'Width'.
   */
  public int getWidth()
  {
    return this._width;
  }

  /**
   * Returns the value of field 'xDim'.
   * 
   * @return the value of field 'XDim'.
   */
  public int getXDim()
  {
    return this._xDim;
  }

  /**
   * Returns the value of field 'xpos'.
   * 
   * @return the value of field 'Xpos'.
   */
  public int getXpos()
  {
    return this._xpos;
  }

  /**
   * Returns the value of field 'yDim'.
   * 
   * @return the value of field 'YDim'.
   */
  public int getYDim()
  {
    return this._yDim;
  }

  /**
   * Returns the value of field 'ypos'.
   * 
   * @return the value of field 'Ypos'.
   */
  public int getYpos()
  {
    return this._ypos;
  }

  /**
   * Returns the value of field 'zDim'.
   * 
   * @return the value of field 'ZDim'.
   */
  public int getZDim()
  {
    return this._zDim;
  }

  /**
   * Method hasBgColour.
   * 
   * @return true if at least one BgColour has been added
   */
  public boolean hasBgColour()
  {
    return this._has_bgColour;
  }

  /**
   * Method hasDenominateByShortestLength.
   * 
   * @return true if at least one DenominateByShortestLength has been added
   */
  public boolean hasDenominateByShortestLength()
  {
    return this._has_denominateByShortestLength;
  }

  /**
   * Method hasHeight.
   * 
   * @return true if at least one Height has been added
   */
  public boolean hasHeight()
  {
    return this._has_height;
  }

  /**
   * Method hasIncludeGappedColumns.
   * 
   * @return true if at least one IncludeGappedColumns has been added
   */
  public boolean hasIncludeGappedColumns()
  {
    return this._has_includeGappedColumns;
  }

  /**
   * Method hasIncludeGaps.
   * 
   * @return true if at least one IncludeGaps has been added
   */
  public boolean hasIncludeGaps()
  {
    return this._has_includeGaps;
  }

  /**
   * Method hasLinkToAllViews.
   * 
   * @return true if at least one LinkToAllViews has been added
   */
  public boolean hasLinkToAllViews()
  {
    return this._has_linkToAllViews;
  }

  /**
   * Method hasMatchGaps.
   * 
   * @return true if at least one MatchGaps has been added
   */
  public boolean hasMatchGaps()
  {
    return this._has_matchGaps;
  }

  /**
   * Method hasScaleFactor.
   * 
   * @return true if at least one ScaleFactor has been added
   */
  public boolean hasScaleFactor()
  {
    return this._has_scaleFactor;
  }

  /**
   * Method hasShowLabels.
   * 
   * @return true if at least one ShowLabels has been added
   */
  public boolean hasShowLabels()
  {
    return this._has_showLabels;
  }

  /**
   * Method hasWidth.
   * 
   * @return true if at least one Width has been added
   */
  public boolean hasWidth()
  {
    return this._has_width;
  }

  /**
   * Method hasXDim.
   * 
   * @return true if at least one XDim has been added
   */
  public boolean hasXDim()
  {
    return this._has_xDim;
  }

  /**
   * Method hasXpos.
   * 
   * @return true if at least one Xpos has been added
   */
  public boolean hasXpos()
  {
    return this._has_xpos;
  }

  /**
   * Method hasYDim.
   * 
   * @return true if at least one YDim has been added
   */
  public boolean hasYDim()
  {
    return this._has_yDim;
  }

  /**
   * Method hasYpos.
   * 
   * @return true if at least one Ypos has been added
   */
  public boolean hasYpos()
  {
    return this._has_ypos;
  }

  /**
   * Method hasZDim.
   * 
   * @return true if at least one ZDim has been added
   */
  public boolean hasZDim()
  {
    return this._has_zDim;
  }

  /**
   * Returns the value of field 'denominateByShortestLength'.
   * 
   * @return the value of field 'DenominateByShortestLength'.
   */
  public boolean isDenominateByShortestLength()
  {
    return this._denominateByShortestLength;
  }

  /**
   * Returns the value of field 'includeGappedColumns'.
   * 
   * @return the value of field 'IncludeGappedColumns'.
   */
  public boolean isIncludeGappedColumns()
  {
    return this._includeGappedColumns;
  }

  /**
   * Returns the value of field 'includeGaps'.
   * 
   * @return the value of field 'IncludeGaps'.
   */
  public boolean isIncludeGaps()
  {
    return this._includeGaps;
  }

  /**
   * Returns the value of field 'linkToAllViews'.
   * 
   * @return the value of field 'LinkToAllViews'.
   */
  public boolean isLinkToAllViews()
  {
    return this._linkToAllViews;
  }

  /**
   * Returns the value of field 'matchGaps'.
   * 
   * @return the value of field 'MatchGaps'.
   */
  public boolean isMatchGaps()
  {
    return this._matchGaps;
  }

  /**
   * Returns the value of field 'showLabels'.
   * 
   * @return the value of field 'ShowLabels'.
   */
  public boolean isShowLabels()
  {
    return this._showLabels;
  }

  /**
   * 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 removeAllAxis()
  {
    this._axisList.clear();
  }

  /**
   */
  public void removeAllSequencePoint()
  {
    this._sequencePointList.clear();
  }

  /**
   * Method removeAxis.
   * 
   * @param vAxis
   * @return true if the object was removed from the collection.
   */
  public boolean removeAxis(final jalview.schemabinding.version2.Axis vAxis)
  {
    boolean removed = _axisList.remove(vAxis);
    return removed;
  }

  /**
   * Method removeAxisAt.
   * 
   * @param index
   * @return the element removed from the collection
   */
  public jalview.schemabinding.version2.Axis removeAxisAt(final int index)
  {
    java.lang.Object obj = this._axisList.remove(index);
    return (jalview.schemabinding.version2.Axis) obj;
  }

  /**
   * Method removeSequencePoint.
   * 
   * @param vSequencePoint
   * @return true if the object was removed from the collection.
   */
  public boolean removeSequencePoint(
          final jalview.schemabinding.version2.SequencePoint vSequencePoint)
  {
    boolean removed = _sequencePointList.remove(vSequencePoint);
    return removed;
  }

  /**
   * Method removeSequencePointAt.
   * 
   * @param index
   * @return the element removed from the collection
   */
  public jalview.schemabinding.version2.SequencePoint removeSequencePointAt(
          final int index)
  {
    java.lang.Object obj = this._sequencePointList.remove(index);
    return (jalview.schemabinding.version2.SequencePoint) obj;
  }

  /**
   * 
   * 
   * @param index
   * @param vAxis
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void setAxis(final int index,
          final jalview.schemabinding.version2.Axis vAxis)
          throws java.lang.IndexOutOfBoundsException
  {
    // check bounds for index
    if (index < 0 || index >= this._axisList.size())
    {
      throw new IndexOutOfBoundsException("setAxis: Index value '" + index
              + "' not in range [0.." + (this._axisList.size() - 1) + "]");
    }

    this._axisList.set(index, vAxis);
  }

  /**
   * 
   * 
   * @param vAxisArray
   */
  public void setAxis(
          final jalview.schemabinding.version2.Axis[] vAxisArray)
  {
    // -- copy array
    _axisList.clear();

    for (int i = 0; i < vAxisArray.length; i++)
    {
      this._axisList.add(vAxisArray[i]);
    }
  }

  /**
   * Sets the value of field 'bgColour'.
   * 
   * @param bgColour
   *          the value of field 'bgColour'.
   */
  public void setBgColour(final int bgColour)
  {
    this._bgColour = bgColour;
    this._has_bgColour = true;
  }

  /**
   * Sets the value of field 'denominateByShortestLength'.
   * 
   * @param denominateByShortestLength
   *          the value of field 'denominateByShortestLength'.
   */
  public void setDenominateByShortestLength(
          final boolean denominateByShortestLength)
  {
    this._denominateByShortestLength = denominateByShortestLength;
    this._has_denominateByShortestLength = true;
  }

  /**
   * Sets the value of field 'height'.
   * 
   * @param height
   *          the value of field 'height'.
   */
  public void setHeight(final int height)
  {
    this._height = height;
    this._has_height = true;
  }

  /**
   * Sets the value of field 'includeGappedColumns'.
   * 
   * @param includeGappedColumns
   *          the value of field 'includeGappedColumns'.
   */
  public void setIncludeGappedColumns(final boolean includeGappedColumns)
  {
    this._includeGappedColumns = includeGappedColumns;
    this._has_includeGappedColumns = true;
  }

  /**
   * Sets the value of field 'includeGaps'.
   * 
   * @param includeGaps
   *          the value of field 'includeGaps'.
   */
  public void setIncludeGaps(final boolean includeGaps)
  {
    this._includeGaps = includeGaps;
    this._has_includeGaps = true;
  }

  /**
   * Sets the value of field 'linkToAllViews'.
   * 
   * @param linkToAllViews
   *          the value of field 'linkToAllViews'.
   */
  public void setLinkToAllViews(final boolean linkToAllViews)
  {
    this._linkToAllViews = linkToAllViews;
    this._has_linkToAllViews = true;
  }

  /**
   * Sets the value of field 'matchGaps'.
   * 
   * @param matchGaps
   *          the value of field 'matchGaps'.
   */
  public void setMatchGaps(final boolean matchGaps)
  {
    this._matchGaps = matchGaps;
    this._has_matchGaps = true;
  }

  /**
   * Sets the value of field 'pcaData'.
   * 
   * @param pcaData
   *          the value of field 'pcaData'.
   */
  public void setPcaData(
          final jalview.schemabinding.version2.PcaData pcaData)
  {
    this._pcaData = pcaData;
  }

  /**
   * Sets the value of field 'scaleFactor'.
   * 
   * @param scaleFactor
   *          the value of field 'scaleFactor'.
   */
  public void setScaleFactor(final float scaleFactor)
  {
    this._scaleFactor = scaleFactor;
    this._has_scaleFactor = true;
  }

  /**
   * Sets the value of field 'scoreModelName'.
   * 
   * @param scoreModelName
   *          the value of field 'scoreModelName'.
   */
  public void setScoreModelName(final java.lang.String scoreModelName)
  {
    this._scoreModelName = scoreModelName;
  }

  /**
   * Sets the value of field 'seqPointMax'.
   * 
   * @param seqPointMax
   *          the value of field 'seqPointMax'.
   */
  public void setSeqPointMax(
          final jalview.schemabinding.version2.SeqPointMax seqPointMax)
  {
    this._seqPointMax = seqPointMax;
  }

  /**
   * Sets the value of field 'seqPointMin'.
   * 
   * @param seqPointMin
   *          the value of field 'seqPointMin'.
   */
  public void setSeqPointMin(
          final jalview.schemabinding.version2.SeqPointMin seqPointMin)
  {
    this._seqPointMin = seqPointMin;
  }

  /**
   * 
   * 
   * @param index
   * @param vSequencePoint
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void setSequencePoint(final int index,
          final jalview.schemabinding.version2.SequencePoint vSequencePoint)
          throws java.lang.IndexOutOfBoundsException
  {
    // check bounds for index
    if (index < 0 || index >= this._sequencePointList.size())
    {
      throw new IndexOutOfBoundsException("setSequencePoint: Index value '"
              + index + "' not in range [0.."
              + (this._sequencePointList.size() - 1) + "]");
    }

    this._sequencePointList.set(index, vSequencePoint);
  }

  /**
   * 
   * 
   * @param vSequencePointArray
   */
  public void setSequencePoint(
          final jalview.schemabinding.version2.SequencePoint[] vSequencePointArray)
  {
    // -- copy array
    _sequencePointList.clear();

    for (int i = 0; i < vSequencePointArray.length; i++)
    {
      this._sequencePointList.add(vSequencePointArray[i]);
    }
  }

  /**
   * Sets the value of field 'showLabels'.
   * 
   * @param showLabels
   *          the value of field 'showLabels'.
   */
  public void setShowLabels(final boolean showLabels)
  {
    this._showLabels = showLabels;
    this._has_showLabels = true;
  }

  /**
   * Sets the value of field 'title'.
   * 
   * @param title
   *          the value of field 'title'.
   */
  public void setTitle(final java.lang.String title)
  {
    this._title = title;
  }

  /**
   * Sets the value of field 'width'.
   * 
   * @param width
   *          the value of field 'width'.
   */
  public void setWidth(final int width)
  {
    this._width = width;
    this._has_width = true;
  }

  /**
   * Sets the value of field 'xDim'.
   * 
   * @param xDim
   *          the value of field 'xDim'.
   */
  public void setXDim(final int xDim)
  {
    this._xDim = xDim;
    this._has_xDim = true;
  }

  /**
   * Sets the value of field 'xpos'.
   * 
   * @param xpos
   *          the value of field 'xpos'.
   */
  public void setXpos(final int xpos)
  {
    this._xpos = xpos;
    this._has_xpos = true;
  }

  /**
   * Sets the value of field 'yDim'.
   * 
   * @param yDim
   *          the value of field 'yDim'.
   */
  public void setYDim(final int yDim)
  {
    this._yDim = yDim;
    this._has_yDim = true;
  }

  /**
   * Sets the value of field 'ypos'.
   * 
   * @param ypos
   *          the value of field 'ypos'.
   */
  public void setYpos(final int ypos)
  {
    this._ypos = ypos;
    this._has_ypos = true;
  }

  /**
   * Sets the value of field 'zDim'.
   * 
   * @param zDim
   *          the value of field 'zDim'.
   */
  public void setZDim(final int zDim)
  {
    this._zDim = zDim;
    this._has_zDim = 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.PcaViewer
   */
  public static jalview.schemabinding.version2.PcaViewer unmarshal(
          final java.io.Reader reader)
          throws org.exolab.castor.xml.MarshalException,
          org.exolab.castor.xml.ValidationException
  {
    return (jalview.schemabinding.version2.PcaViewer) Unmarshaller
            .unmarshal(jalview.schemabinding.version2.PcaViewer.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);
  }

}