JAL-958 store normalised flag in jalview project

[jalview.git] / src / jalview / schemabinding / version2 / Viewport.java

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


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

    /**
     * Field _conservationSelected.
     */
    private boolean _conservationSelected;

    /**
     * keeps track of state for field: _conservationSelected
     */
    private boolean _has_conservationSelected;

    /**
     * Field _pidSelected.
     */
    private boolean _pidSelected;

    /**
     * keeps track of state for field: _pidSelected
     */
    private boolean _has_pidSelected;

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

    /**
     * Field _consThreshold.
     */
    private int _consThreshold;

    /**
     * keeps track of state for field: _consThreshold
     */
    private boolean _has_consThreshold;

    /**
     * Field _pidThreshold.
     */
    private int _pidThreshold;

    /**
     * keeps track of state for field: _pidThreshold
     */
    private boolean _has_pidThreshold;

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

    /**
     * Field _showFullId.
     */
    private boolean _showFullId;

    /**
     * keeps track of state for field: _showFullId
     */
    private boolean _has_showFullId;

    /**
     * Field _rightAlignIds.
     */
    private boolean _rightAlignIds;

    /**
     * keeps track of state for field: _rightAlignIds
     */
    private boolean _has_rightAlignIds;

    /**
     * Field _showText.
     */
    private boolean _showText;

    /**
     * keeps track of state for field: _showText
     */
    private boolean _has_showText;

    /**
     * Field _showColourText.
     */
    private boolean _showColourText;

    /**
     * keeps track of state for field: _showColourText
     */
    private boolean _has_showColourText;

    /**
     * Field _showUnconserved.
     */
    private boolean _showUnconserved = false;

    /**
     * keeps track of state for field: _showUnconserved
     */
    private boolean _has_showUnconserved;

    /**
     * Field _showBoxes.
     */
    private boolean _showBoxes;

    /**
     * keeps track of state for field: _showBoxes
     */
    private boolean _has_showBoxes;

    /**
     * Field _wrapAlignment.
     */
    private boolean _wrapAlignment;

    /**
     * keeps track of state for field: _wrapAlignment
     */
    private boolean _has_wrapAlignment;

    /**
     * Field _renderGaps.
     */
    private boolean _renderGaps;

    /**
     * keeps track of state for field: _renderGaps
     */
    private boolean _has_renderGaps;

    /**
     * Field _showSequenceFeatures.
     */
    private boolean _showSequenceFeatures;

    /**
     * keeps track of state for field: _showSequenceFeatures
     */
    private boolean _has_showSequenceFeatures;

    /**
     * Field _showNPfeatureTooltip.
     */
    private boolean _showNPfeatureTooltip;

    /**
     * keeps track of state for field: _showNPfeatureTooltip
     */
    private boolean _has_showNPfeatureTooltip;

    /**
     * Field _showDbRefTooltip.
     */
    private boolean _showDbRefTooltip;

    /**
     * keeps track of state for field: _showDbRefTooltip
     */
    private boolean _has_showDbRefTooltip;

    /**
     * Field _followHighlight.
     */
    private boolean _followHighlight = true;

    /**
     * keeps track of state for field: _followHighlight
     */
    private boolean _has_followHighlight;

    /**
     * Field _followSelection.
     */
    private boolean _followSelection = true;

    /**
     * keeps track of state for field: _followSelection
     */
    private boolean _has_followSelection;

    /**
     * Field _showAnnotation.
     */
    private boolean _showAnnotation;

    /**
     * keeps track of state for field: _showAnnotation
     */
    private boolean _has_showAnnotation;

    /**
     * Field _centreColumnLabels.
     */
    private boolean _centreColumnLabels = false;

    /**
     * keeps track of state for field: _centreColumnLabels
     */
    private boolean _has_centreColumnLabels;

    /**
     * Field _showGroupConservation.
     */
    private boolean _showGroupConservation = false;

    /**
     * keeps track of state for field: _showGroupConservation
     */
    private boolean _has_showGroupConservation;

    /**
     * Field _showGroupConsensus.
     */
    private boolean _showGroupConsensus = false;

    /**
     * keeps track of state for field: _showGroupConsensus
     */
    private boolean _has_showGroupConsensus;

    /**
     * Field _showConsensusHistogram.
     */
    private boolean _showConsensusHistogram = true;

    /**
     * keeps track of state for field: _showConsensusHistogram
     */
    private boolean _has_showConsensusHistogram;

    /**
     * Field _showSequenceLogo.
     */
    private boolean _showSequenceLogo = false;

    /**
     * keeps track of state for field: _showSequenceLogo
     */
    private boolean _has_showSequenceLogo;

    /**
     * Field _normaliseSequenceLogo.
     */
    private boolean _normaliseSequenceLogo = false;

    /**
     * keeps track of state for field: _normaliseSequenceLogo
     */
    private boolean _has_normaliseSequenceLogo;

    /**
     * Field _ignoreGapsinConsensus.
     */
    private boolean _ignoreGapsinConsensus = true;

    /**
     * keeps track of state for field: _ignoreGapsinConsensus
     */
    private boolean _has_ignoreGapsinConsensus;

    /**
     * Field _startRes.
     */
    private int _startRes;

    /**
     * keeps track of state for field: _startRes
     */
    private boolean _has_startRes;

    /**
     * Field _startSeq.
     */
    private int _startSeq;

    /**
     * keeps track of state for field: _startSeq
     */
    private boolean _has_startSeq;

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

    /**
     * Field _fontSize.
     */
    private int _fontSize;

    /**
     * keeps track of state for field: _fontSize
     */
    private boolean _has_fontSize;

    /**
     * Field _fontStyle.
     */
    private int _fontStyle;

    /**
     * keeps track of state for field: _fontStyle
     */
    private boolean _has_fontStyle;

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

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

    /**
     * Field _gatheredViews.
     */
    private boolean _gatheredViews;

    /**
     * keeps track of state for field: _gatheredViews
     */
    private boolean _has_gatheredViews;

    /**
     * Field _textCol1.
     */
    private int _textCol1;

    /**
     * keeps track of state for field: _textCol1
     */
    private boolean _has_textCol1;

    /**
     * Field _textCol2.
     */
    private int _textCol2;

    /**
     * keeps track of state for field: _textCol2
     */
    private boolean _has_textCol2;

    /**
     * Field _textColThreshold.
     */
    private int _textColThreshold;

    /**
     * keeps track of state for field: _textColThreshold
     */
    private boolean _has_textColThreshold;

    /**
     * unique id used by jalview to
     *  synchronize between stored and
     *  instantiated views
     *  
     */
    private java.lang.String _id;

    /**
     * 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 _annotationColours.
     */
    private jalview.schemabinding.version2.AnnotationColours _annotationColours;

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

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


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

    public Viewport() {
        super();
        this._hiddenColumnsList = new java.util.Vector();
        this._calcIdParamList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vCalcIdParam
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addCalcIdParam(
            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
    throws java.lang.IndexOutOfBoundsException {
        this._calcIdParamList.addElement(vCalcIdParam);
    }

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

    /**
     * 
     * 
     * @param vHiddenColumns
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addHiddenColumns(
            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
    throws java.lang.IndexOutOfBoundsException {
        this._hiddenColumnsList.addElement(vHiddenColumns);
    }

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

    /**
     */
    public void deleteCentreColumnLabels(
    ) {
        this._has_centreColumnLabels= false;
    }

    /**
     */
    public void deleteConsThreshold(
    ) {
        this._has_consThreshold= false;
    }

    /**
     */
    public void deleteConservationSelected(
    ) {
        this._has_conservationSelected= false;
    }

    /**
     */
    public void deleteFollowHighlight(
    ) {
        this._has_followHighlight= false;
    }

    /**
     */
    public void deleteFollowSelection(
    ) {
        this._has_followSelection= false;
    }

    /**
     */
    public void deleteFontSize(
    ) {
        this._has_fontSize= false;
    }

    /**
     */
    public void deleteFontStyle(
    ) {
        this._has_fontStyle= false;
    }

    /**
     */
    public void deleteGatheredViews(
    ) {
        this._has_gatheredViews= false;
    }

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

    /**
     */
    public void deleteIgnoreGapsinConsensus(
    ) {
        this._has_ignoreGapsinConsensus= false;
    }

    /**
     */
    public void deleteNormaliseSequenceLogo(
    ) {
        this._has_normaliseSequenceLogo= false;
    }

    /**
     */
    public void deletePidSelected(
    ) {
        this._has_pidSelected= false;
    }

    /**
     */
    public void deletePidThreshold(
    ) {
        this._has_pidThreshold= false;
    }

    /**
     */
    public void deleteRenderGaps(
    ) {
        this._has_renderGaps= false;
    }

    /**
     */
    public void deleteRightAlignIds(
    ) {
        this._has_rightAlignIds= false;
    }

    /**
     */
    public void deleteShowAnnotation(
    ) {
        this._has_showAnnotation= false;
    }

    /**
     */
    public void deleteShowBoxes(
    ) {
        this._has_showBoxes= false;
    }

    /**
     */
    public void deleteShowColourText(
    ) {
        this._has_showColourText= false;
    }

    /**
     */
    public void deleteShowConsensusHistogram(
    ) {
        this._has_showConsensusHistogram= false;
    }

    /**
     */
    public void deleteShowDbRefTooltip(
    ) {
        this._has_showDbRefTooltip= false;
    }

    /**
     */
    public void deleteShowFullId(
    ) {
        this._has_showFullId= false;
    }

    /**
     */
    public void deleteShowGroupConsensus(
    ) {
        this._has_showGroupConsensus= false;
    }

    /**
     */
    public void deleteShowGroupConservation(
    ) {
        this._has_showGroupConservation= false;
    }

    /**
     */
    public void deleteShowNPfeatureTooltip(
    ) {
        this._has_showNPfeatureTooltip= false;
    }

    /**
     */
    public void deleteShowSequenceFeatures(
    ) {
        this._has_showSequenceFeatures= false;
    }

    /**
     */
    public void deleteShowSequenceLogo(
    ) {
        this._has_showSequenceLogo= false;
    }

    /**
     */
    public void deleteShowText(
    ) {
        this._has_showText= false;
    }

    /**
     */
    public void deleteShowUnconserved(
    ) {
        this._has_showUnconserved= false;
    }

    /**
     */
    public void deleteStartRes(
    ) {
        this._has_startRes= false;
    }

    /**
     */
    public void deleteStartSeq(
    ) {
        this._has_startSeq= false;
    }

    /**
     */
    public void deleteTextCol1(
    ) {
        this._has_textCol1= false;
    }

    /**
     */
    public void deleteTextCol2(
    ) {
        this._has_textCol2= false;
    }

    /**
     */
    public void deleteTextColThreshold(
    ) {
        this._has_textColThreshold= false;
    }

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

    /**
     */
    public void deleteWrapAlignment(
    ) {
        this._has_wrapAlignment= false;
    }

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

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

    /**
     * Method enumerateCalcIdParam.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.CalcIdParam elements
     */
    public java.util.Enumeration enumerateCalcIdParam(
    ) {
        return this._calcIdParamList.elements();
    }

    /**
     * Method enumerateHiddenColumns.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.HiddenColumns elements
     */
    public java.util.Enumeration enumerateHiddenColumns(
    ) {
        return this._hiddenColumnsList.elements();
    }

    /**
     * Returns the value of field 'annotationColours'.
     * 
     * @return the value of field 'AnnotationColours'.
     */
    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
    ) {
        return this._annotationColours;
    }

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

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

    /**
     * Method getCalcIdParam.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.CalcIdParam[] getCalcIdParam(
    ) {
        jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
        return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
    }

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

    /**
     * Returns the value of field 'centreColumnLabels'.
     * 
     * @return the value of field 'CentreColumnLabels'.
     */
    public boolean getCentreColumnLabels(
    ) {
        return this._centreColumnLabels;
    }

    /**
     * Returns the value of field 'consThreshold'.
     * 
     * @return the value of field 'ConsThreshold'.
     */
    public int getConsThreshold(
    ) {
        return this._consThreshold;
    }

    /**
     * Returns the value of field 'conservationSelected'.
     * 
     * @return the value of field 'ConservationSelected'.
     */
    public boolean getConservationSelected(
    ) {
        return this._conservationSelected;
    }

    /**
     * Returns the value of field 'followHighlight'.
     * 
     * @return the value of field 'FollowHighlight'.
     */
    public boolean getFollowHighlight(
    ) {
        return this._followHighlight;
    }

    /**
     * Returns the value of field 'followSelection'.
     * 
     * @return the value of field 'FollowSelection'.
     */
    public boolean getFollowSelection(
    ) {
        return this._followSelection;
    }

    /**
     * Returns the value of field 'fontName'.
     * 
     * @return the value of field 'FontName'.
     */
    public java.lang.String getFontName(
    ) {
        return this._fontName;
    }

    /**
     * Returns the value of field 'fontSize'.
     * 
     * @return the value of field 'FontSize'.
     */
    public int getFontSize(
    ) {
        return this._fontSize;
    }

    /**
     * Returns the value of field 'fontStyle'.
     * 
     * @return the value of field 'FontStyle'.
     */
    public int getFontStyle(
    ) {
        return this._fontStyle;
    }

    /**
     * Returns the value of field 'gatheredViews'.
     * 
     * @return the value of field 'GatheredViews'.
     */
    public boolean getGatheredViews(
    ) {
        return this._gatheredViews;
    }

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

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

    /**
     * Method getHiddenColumns.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.HiddenColumns[] getHiddenColumns(
    ) {
        jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
        return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
    }

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

    /**
     * Returns the value of field 'id'. The field 'id' has the
     * following description: unique id used by jalview to
     *  synchronize between stored and
     *  instantiated views
     *  
     * 
     * @return the value of field 'Id'.
     */
    public java.lang.String getId(
    ) {
        return this._id;
    }

    /**
     * Returns the value of field 'ignoreGapsinConsensus'.
     * 
     * @return the value of field 'IgnoreGapsinConsensus'.
     */
    public boolean getIgnoreGapsinConsensus(
    ) {
        return this._ignoreGapsinConsensus;
    }

    /**
     * Returns the value of field 'normaliseSequenceLogo'.
     * 
     * @return the value of field 'NormaliseSequenceLogo'.
     */
    public boolean getNormaliseSequenceLogo(
    ) {
        return this._normaliseSequenceLogo;
    }

    /**
     * Returns the value of field 'pidSelected'.
     * 
     * @return the value of field 'PidSelected'.
     */
    public boolean getPidSelected(
    ) {
        return this._pidSelected;
    }

    /**
     * Returns the value of field 'pidThreshold'.
     * 
     * @return the value of field 'PidThreshold'.
     */
    public int getPidThreshold(
    ) {
        return this._pidThreshold;
    }

    /**
     * Returns the value of field 'renderGaps'.
     * 
     * @return the value of field 'RenderGaps'.
     */
    public boolean getRenderGaps(
    ) {
        return this._renderGaps;
    }

    /**
     * Returns the value of field 'rightAlignIds'.
     * 
     * @return the value of field 'RightAlignIds'.
     */
    public boolean getRightAlignIds(
    ) {
        return this._rightAlignIds;
    }

    /**
     * Returns the value of field 'sequenceSetId'.
     * 
     * @return the value of field 'SequenceSetId'.
     */
    public java.lang.String getSequenceSetId(
    ) {
        return this._sequenceSetId;
    }

    /**
     * Returns the value of field 'showAnnotation'.
     * 
     * @return the value of field 'ShowAnnotation'.
     */
    public boolean getShowAnnotation(
    ) {
        return this._showAnnotation;
    }

    /**
     * Returns the value of field 'showBoxes'.
     * 
     * @return the value of field 'ShowBoxes'.
     */
    public boolean getShowBoxes(
    ) {
        return this._showBoxes;
    }

    /**
     * Returns the value of field 'showColourText'.
     * 
     * @return the value of field 'ShowColourText'.
     */
    public boolean getShowColourText(
    ) {
        return this._showColourText;
    }

    /**
     * Returns the value of field 'showConsensusHistogram'.
     * 
     * @return the value of field 'ShowConsensusHistogram'.
     */
    public boolean getShowConsensusHistogram(
    ) {
        return this._showConsensusHistogram;
    }

    /**
     * Returns the value of field 'showDbRefTooltip'.
     * 
     * @return the value of field 'ShowDbRefTooltip'.
     */
    public boolean getShowDbRefTooltip(
    ) {
        return this._showDbRefTooltip;
    }

    /**
     * Returns the value of field 'showFullId'.
     * 
     * @return the value of field 'ShowFullId'.
     */
    public boolean getShowFullId(
    ) {
        return this._showFullId;
    }

    /**
     * Returns the value of field 'showGroupConsensus'.
     * 
     * @return the value of field 'ShowGroupConsensus'.
     */
    public boolean getShowGroupConsensus(
    ) {
        return this._showGroupConsensus;
    }

    /**
     * Returns the value of field 'showGroupConservation'.
     * 
     * @return the value of field 'ShowGroupConservation'.
     */
    public boolean getShowGroupConservation(
    ) {
        return this._showGroupConservation;
    }

    /**
     * Returns the value of field 'showNPfeatureTooltip'.
     * 
     * @return the value of field 'ShowNPfeatureTooltip'.
     */
    public boolean getShowNPfeatureTooltip(
    ) {
        return this._showNPfeatureTooltip;
    }

    /**
     * Returns the value of field 'showSequenceFeatures'.
     * 
     * @return the value of field 'ShowSequenceFeatures'.
     */
    public boolean getShowSequenceFeatures(
    ) {
        return this._showSequenceFeatures;
    }

    /**
     * Returns the value of field 'showSequenceLogo'.
     * 
     * @return the value of field 'ShowSequenceLogo'.
     */
    public boolean getShowSequenceLogo(
    ) {
        return this._showSequenceLogo;
    }

    /**
     * Returns the value of field 'showText'.
     * 
     * @return the value of field 'ShowText'.
     */
    public boolean getShowText(
    ) {
        return this._showText;
    }

    /**
     * Returns the value of field 'showUnconserved'.
     * 
     * @return the value of field 'ShowUnconserved'.
     */
    public boolean getShowUnconserved(
    ) {
        return this._showUnconserved;
    }

    /**
     * Returns the value of field 'startRes'.
     * 
     * @return the value of field 'StartRes'.
     */
    public int getStartRes(
    ) {
        return this._startRes;
    }

    /**
     * Returns the value of field 'startSeq'.
     * 
     * @return the value of field 'StartSeq'.
     */
    public int getStartSeq(
    ) {
        return this._startSeq;
    }

    /**
     * Returns the value of field 'textCol1'.
     * 
     * @return the value of field 'TextCol1'.
     */
    public int getTextCol1(
    ) {
        return this._textCol1;
    }

    /**
     * Returns the value of field 'textCol2'.
     * 
     * @return the value of field 'TextCol2'.
     */
    public int getTextCol2(
    ) {
        return this._textCol2;
    }

    /**
     * Returns the value of field 'textColThreshold'.
     * 
     * @return the value of field 'TextColThreshold'.
     */
    public int getTextColThreshold(
    ) {
        return this._textColThreshold;
    }

    /**
     * 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 'viewName'.
     * 
     * @return the value of field 'ViewName'.
     */
    public java.lang.String getViewName(
    ) {
        return this._viewName;
    }

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

    /**
     * Returns the value of field 'wrapAlignment'.
     * 
     * @return the value of field 'WrapAlignment'.
     */
    public boolean getWrapAlignment(
    ) {
        return this._wrapAlignment;
    }

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

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

    /**
     * Method hasCentreColumnLabels.
     * 
     * @return true if at least one CentreColumnLabels has been adde
     */
    public boolean hasCentreColumnLabels(
    ) {
        return this._has_centreColumnLabels;
    }

    /**
     * Method hasConsThreshold.
     * 
     * @return true if at least one ConsThreshold has been added
     */
    public boolean hasConsThreshold(
    ) {
        return this._has_consThreshold;
    }

    /**
     * Method hasConservationSelected.
     * 
     * @return true if at least one ConservationSelected has been
     * added
     */
    public boolean hasConservationSelected(
    ) {
        return this._has_conservationSelected;
    }

    /**
     * Method hasFollowHighlight.
     * 
     * @return true if at least one FollowHighlight has been added
     */
    public boolean hasFollowHighlight(
    ) {
        return this._has_followHighlight;
    }

    /**
     * Method hasFollowSelection.
     * 
     * @return true if at least one FollowSelection has been added
     */
    public boolean hasFollowSelection(
    ) {
        return this._has_followSelection;
    }

    /**
     * Method hasFontSize.
     * 
     * @return true if at least one FontSize has been added
     */
    public boolean hasFontSize(
    ) {
        return this._has_fontSize;
    }

    /**
     * Method hasFontStyle.
     * 
     * @return true if at least one FontStyle has been added
     */
    public boolean hasFontStyle(
    ) {
        return this._has_fontStyle;
    }

    /**
     * Method hasGatheredViews.
     * 
     * @return true if at least one GatheredViews has been added
     */
    public boolean hasGatheredViews(
    ) {
        return this._has_gatheredViews;
    }

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

    /**
     * Method hasIgnoreGapsinConsensus.
     * 
     * @return true if at least one IgnoreGapsinConsensus has been
     * added
     */
    public boolean hasIgnoreGapsinConsensus(
    ) {
        return this._has_ignoreGapsinConsensus;
    }

    /**
     * Method hasNormaliseSequenceLogo.
     * 
     * @return true if at least one NormaliseSequenceLogo has been
     * added
     */
    public boolean hasNormaliseSequenceLogo(
    ) {
        return this._has_normaliseSequenceLogo;
    }

    /**
     * Method hasPidSelected.
     * 
     * @return true if at least one PidSelected has been added
     */
    public boolean hasPidSelected(
    ) {
        return this._has_pidSelected;
    }

    /**
     * Method hasPidThreshold.
     * 
     * @return true if at least one PidThreshold has been added
     */
    public boolean hasPidThreshold(
    ) {
        return this._has_pidThreshold;
    }

    /**
     * Method hasRenderGaps.
     * 
     * @return true if at least one RenderGaps has been added
     */
    public boolean hasRenderGaps(
    ) {
        return this._has_renderGaps;
    }

    /**
     * Method hasRightAlignIds.
     * 
     * @return true if at least one RightAlignIds has been added
     */
    public boolean hasRightAlignIds(
    ) {
        return this._has_rightAlignIds;
    }

    /**
     * Method hasShowAnnotation.
     * 
     * @return true if at least one ShowAnnotation has been added
     */
    public boolean hasShowAnnotation(
    ) {
        return this._has_showAnnotation;
    }

    /**
     * Method hasShowBoxes.
     * 
     * @return true if at least one ShowBoxes has been added
     */
    public boolean hasShowBoxes(
    ) {
        return this._has_showBoxes;
    }

    /**
     * Method hasShowColourText.
     * 
     * @return true if at least one ShowColourText has been added
     */
    public boolean hasShowColourText(
    ) {
        return this._has_showColourText;
    }

    /**
     * Method hasShowConsensusHistogram.
     * 
     * @return true if at least one ShowConsensusHistogram has been
     * added
     */
    public boolean hasShowConsensusHistogram(
    ) {
        return this._has_showConsensusHistogram;
    }

    /**
     * Method hasShowDbRefTooltip.
     * 
     * @return true if at least one ShowDbRefTooltip has been added
     */
    public boolean hasShowDbRefTooltip(
    ) {
        return this._has_showDbRefTooltip;
    }

    /**
     * Method hasShowFullId.
     * 
     * @return true if at least one ShowFullId has been added
     */
    public boolean hasShowFullId(
    ) {
        return this._has_showFullId;
    }

    /**
     * Method hasShowGroupConsensus.
     * 
     * @return true if at least one ShowGroupConsensus has been adde
     */
    public boolean hasShowGroupConsensus(
    ) {
        return this._has_showGroupConsensus;
    }

    /**
     * Method hasShowGroupConservation.
     * 
     * @return true if at least one ShowGroupConservation has been
     * added
     */
    public boolean hasShowGroupConservation(
    ) {
        return this._has_showGroupConservation;
    }

    /**
     * Method hasShowNPfeatureTooltip.
     * 
     * @return true if at least one ShowNPfeatureTooltip has been
     * added
     */
    public boolean hasShowNPfeatureTooltip(
    ) {
        return this._has_showNPfeatureTooltip;
    }

    /**
     * Method hasShowSequenceFeatures.
     * 
     * @return true if at least one ShowSequenceFeatures has been
     * added
     */
    public boolean hasShowSequenceFeatures(
    ) {
        return this._has_showSequenceFeatures;
    }

    /**
     * Method hasShowSequenceLogo.
     * 
     * @return true if at least one ShowSequenceLogo has been added
     */
    public boolean hasShowSequenceLogo(
    ) {
        return this._has_showSequenceLogo;
    }

    /**
     * Method hasShowText.
     * 
     * @return true if at least one ShowText has been added
     */
    public boolean hasShowText(
    ) {
        return this._has_showText;
    }

    /**
     * Method hasShowUnconserved.
     * 
     * @return true if at least one ShowUnconserved has been added
     */
    public boolean hasShowUnconserved(
    ) {
        return this._has_showUnconserved;
    }

    /**
     * Method hasStartRes.
     * 
     * @return true if at least one StartRes has been added
     */
    public boolean hasStartRes(
    ) {
        return this._has_startRes;
    }

    /**
     * Method hasStartSeq.
     * 
     * @return true if at least one StartSeq has been added
     */
    public boolean hasStartSeq(
    ) {
        return this._has_startSeq;
    }

    /**
     * Method hasTextCol1.
     * 
     * @return true if at least one TextCol1 has been added
     */
    public boolean hasTextCol1(
    ) {
        return this._has_textCol1;
    }

    /**
     * Method hasTextCol2.
     * 
     * @return true if at least one TextCol2 has been added
     */
    public boolean hasTextCol2(
    ) {
        return this._has_textCol2;
    }

    /**
     * Method hasTextColThreshold.
     * 
     * @return true if at least one TextColThreshold has been added
     */
    public boolean hasTextColThreshold(
    ) {
        return this._has_textColThreshold;
    }

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

    /**
     * Method hasWrapAlignment.
     * 
     * @return true if at least one WrapAlignment has been added
     */
    public boolean hasWrapAlignment(
    ) {
        return this._has_wrapAlignment;
    }

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

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

    /**
     * Returns the value of field 'centreColumnLabels'.
     * 
     * @return the value of field 'CentreColumnLabels'.
     */
    public boolean isCentreColumnLabels(
    ) {
        return this._centreColumnLabels;
    }

    /**
     * Returns the value of field 'conservationSelected'.
     * 
     * @return the value of field 'ConservationSelected'.
     */
    public boolean isConservationSelected(
    ) {
        return this._conservationSelected;
    }

    /**
     * Returns the value of field 'followHighlight'.
     * 
     * @return the value of field 'FollowHighlight'.
     */
    public boolean isFollowHighlight(
    ) {
        return this._followHighlight;
    }

    /**
     * Returns the value of field 'followSelection'.
     * 
     * @return the value of field 'FollowSelection'.
     */
    public boolean isFollowSelection(
    ) {
        return this._followSelection;
    }

    /**
     * Returns the value of field 'gatheredViews'.
     * 
     * @return the value of field 'GatheredViews'.
     */
    public boolean isGatheredViews(
    ) {
        return this._gatheredViews;
    }

    /**
     * Returns the value of field 'ignoreGapsinConsensus'.
     * 
     * @return the value of field 'IgnoreGapsinConsensus'.
     */
    public boolean isIgnoreGapsinConsensus(
    ) {
        return this._ignoreGapsinConsensus;
    }

    /**
     * Returns the value of field 'normaliseSequenceLogo'.
     * 
     * @return the value of field 'NormaliseSequenceLogo'.
     */
    public boolean isNormaliseSequenceLogo(
    ) {
        return this._normaliseSequenceLogo;
    }

    /**
     * Returns the value of field 'pidSelected'.
     * 
     * @return the value of field 'PidSelected'.
     */
    public boolean isPidSelected(
    ) {
        return this._pidSelected;
    }

    /**
     * Returns the value of field 'renderGaps'.
     * 
     * @return the value of field 'RenderGaps'.
     */
    public boolean isRenderGaps(
    ) {
        return this._renderGaps;
    }

    /**
     * Returns the value of field 'rightAlignIds'.
     * 
     * @return the value of field 'RightAlignIds'.
     */
    public boolean isRightAlignIds(
    ) {
        return this._rightAlignIds;
    }

    /**
     * Returns the value of field 'showAnnotation'.
     * 
     * @return the value of field 'ShowAnnotation'.
     */
    public boolean isShowAnnotation(
    ) {
        return this._showAnnotation;
    }

    /**
     * Returns the value of field 'showBoxes'.
     * 
     * @return the value of field 'ShowBoxes'.
     */
    public boolean isShowBoxes(
    ) {
        return this._showBoxes;
    }

    /**
     * Returns the value of field 'showColourText'.
     * 
     * @return the value of field 'ShowColourText'.
     */
    public boolean isShowColourText(
    ) {
        return this._showColourText;
    }

    /**
     * Returns the value of field 'showConsensusHistogram'.
     * 
     * @return the value of field 'ShowConsensusHistogram'.
     */
    public boolean isShowConsensusHistogram(
    ) {
        return this._showConsensusHistogram;
    }

    /**
     * Returns the value of field 'showDbRefTooltip'.
     * 
     * @return the value of field 'ShowDbRefTooltip'.
     */
    public boolean isShowDbRefTooltip(
    ) {
        return this._showDbRefTooltip;
    }

    /**
     * Returns the value of field 'showFullId'.
     * 
     * @return the value of field 'ShowFullId'.
     */
    public boolean isShowFullId(
    ) {
        return this._showFullId;
    }

    /**
     * Returns the value of field 'showGroupConsensus'.
     * 
     * @return the value of field 'ShowGroupConsensus'.
     */
    public boolean isShowGroupConsensus(
    ) {
        return this._showGroupConsensus;
    }

    /**
     * Returns the value of field 'showGroupConservation'.
     * 
     * @return the value of field 'ShowGroupConservation'.
     */
    public boolean isShowGroupConservation(
    ) {
        return this._showGroupConservation;
    }

    /**
     * Returns the value of field 'showNPfeatureTooltip'.
     * 
     * @return the value of field 'ShowNPfeatureTooltip'.
     */
    public boolean isShowNPfeatureTooltip(
    ) {
        return this._showNPfeatureTooltip;
    }

    /**
     * Returns the value of field 'showSequenceFeatures'.
     * 
     * @return the value of field 'ShowSequenceFeatures'.
     */
    public boolean isShowSequenceFeatures(
    ) {
        return this._showSequenceFeatures;
    }

    /**
     * Returns the value of field 'showSequenceLogo'.
     * 
     * @return the value of field 'ShowSequenceLogo'.
     */
    public boolean isShowSequenceLogo(
    ) {
        return this._showSequenceLogo;
    }

    /**
     * Returns the value of field 'showText'.
     * 
     * @return the value of field 'ShowText'.
     */
    public boolean isShowText(
    ) {
        return this._showText;
    }

    /**
     * Returns the value of field 'showUnconserved'.
     * 
     * @return the value of field 'ShowUnconserved'.
     */
    public boolean isShowUnconserved(
    ) {
        return this._showUnconserved;
    }

    /**
     * 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 'wrapAlignment'.
     * 
     * @return the value of field 'WrapAlignment'.
     */
    public boolean isWrapAlignment(
    ) {
        return this._wrapAlignment;
    }

    /**
     * 
     * 
     * @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 removeAllCalcIdParam(
    ) {
        this._calcIdParamList.clear();
    }

    /**
     */
    public void removeAllHiddenColumns(
    ) {
        this._hiddenColumnsList.clear();
    }

    /**
     * Method removeCalcIdParam.
     * 
     * @param vCalcIdParam
     * @return true if the object was removed from the collection.
     */
    public boolean removeCalcIdParam(
            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
        boolean removed = _calcIdParamList.remove(vCalcIdParam);
        return removed;
    }

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

    /**
     * Method removeHiddenColumns.
     * 
     * @param vHiddenColumns
     * @return true if the object was removed from the collection.
     */
    public boolean removeHiddenColumns(
            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
        boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
        return removed;
    }

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

    /**
     * Sets the value of field 'annotationColours'.
     * 
     * @param annotationColours the value of field
     * 'annotationColours'.
     */
    public void setAnnotationColours(
            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
        this._annotationColours = annotationColours;
    }

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

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

    /**
     * 
     * 
     * @param vCalcIdParamArray
     */
    public void setCalcIdParam(
            final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
        //-- copy array
        _calcIdParamList.clear();
        
        for (int i = 0; i < vCalcIdParamArray.length; i++) {
                this._calcIdParamList.add(vCalcIdParamArray[i]);
        }
    }

    /**
     * Sets the value of field 'centreColumnLabels'.
     * 
     * @param centreColumnLabels the value of field
     * 'centreColumnLabels'.
     */
    public void setCentreColumnLabels(
            final boolean centreColumnLabels) {
        this._centreColumnLabels = centreColumnLabels;
        this._has_centreColumnLabels = true;
    }

    /**
     * Sets the value of field 'consThreshold'.
     * 
     * @param consThreshold the value of field 'consThreshold'.
     */
    public void setConsThreshold(
            final int consThreshold) {
        this._consThreshold = consThreshold;
        this._has_consThreshold = true;
    }

    /**
     * Sets the value of field 'conservationSelected'.
     * 
     * @param conservationSelected the value of field
     * 'conservationSelected'.
     */
    public void setConservationSelected(
            final boolean conservationSelected) {
        this._conservationSelected = conservationSelected;
        this._has_conservationSelected = true;
    }

    /**
     * Sets the value of field 'followHighlight'.
     * 
     * @param followHighlight the value of field 'followHighlight'.
     */
    public void setFollowHighlight(
            final boolean followHighlight) {
        this._followHighlight = followHighlight;
        this._has_followHighlight = true;
    }

    /**
     * Sets the value of field 'followSelection'.
     * 
     * @param followSelection the value of field 'followSelection'.
     */
    public void setFollowSelection(
            final boolean followSelection) {
        this._followSelection = followSelection;
        this._has_followSelection = true;
    }

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

    /**
     * Sets the value of field 'fontSize'.
     * 
     * @param fontSize the value of field 'fontSize'.
     */
    public void setFontSize(
            final int fontSize) {
        this._fontSize = fontSize;
        this._has_fontSize = true;
    }

    /**
     * Sets the value of field 'fontStyle'.
     * 
     * @param fontStyle the value of field 'fontStyle'.
     */
    public void setFontStyle(
            final int fontStyle) {
        this._fontStyle = fontStyle;
        this._has_fontStyle = true;
    }

    /**
     * Sets the value of field 'gatheredViews'.
     * 
     * @param gatheredViews the value of field 'gatheredViews'.
     */
    public void setGatheredViews(
            final boolean gatheredViews) {
        this._gatheredViews = gatheredViews;
        this._has_gatheredViews = 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;
    }

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

    /**
     * 
     * 
     * @param vHiddenColumnsArray
     */
    public void setHiddenColumns(
            final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
        //-- copy array
        _hiddenColumnsList.clear();
        
        for (int i = 0; i < vHiddenColumnsArray.length; i++) {
                this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
        }
    }

    /**
     * Sets the value of field 'id'. The field 'id' has the
     * following description: unique id used by jalview to
     *  synchronize between stored and
     *  instantiated views
     *  
     * 
     * @param id the value of field 'id'.
     */
    public void setId(
            final java.lang.String id) {
        this._id = id;
    }

    /**
     * Sets the value of field 'ignoreGapsinConsensus'.
     * 
     * @param ignoreGapsinConsensus the value of field
     * 'ignoreGapsinConsensus'.
     */
    public void setIgnoreGapsinConsensus(
            final boolean ignoreGapsinConsensus) {
        this._ignoreGapsinConsensus = ignoreGapsinConsensus;
        this._has_ignoreGapsinConsensus = true;
    }

    /**
     * Sets the value of field 'normaliseSequenceLogo'.
     * 
     * @param normaliseSequenceLogo the value of field
     * 'normaliseSequenceLogo'.
     */
    public void setNormaliseSequenceLogo(
            final boolean normaliseSequenceLogo) {
        this._normaliseSequenceLogo = normaliseSequenceLogo;
        this._has_normaliseSequenceLogo = true;
    }

    /**
     * Sets the value of field 'pidSelected'.
     * 
     * @param pidSelected the value of field 'pidSelected'.
     */
    public void setPidSelected(
            final boolean pidSelected) {
        this._pidSelected = pidSelected;
        this._has_pidSelected = true;
    }

    /**
     * Sets the value of field 'pidThreshold'.
     * 
     * @param pidThreshold the value of field 'pidThreshold'.
     */
    public void setPidThreshold(
            final int pidThreshold) {
        this._pidThreshold = pidThreshold;
        this._has_pidThreshold = true;
    }

    /**
     * Sets the value of field 'renderGaps'.
     * 
     * @param renderGaps the value of field 'renderGaps'.
     */
    public void setRenderGaps(
            final boolean renderGaps) {
        this._renderGaps = renderGaps;
        this._has_renderGaps = true;
    }

    /**
     * Sets the value of field 'rightAlignIds'.
     * 
     * @param rightAlignIds the value of field 'rightAlignIds'.
     */
    public void setRightAlignIds(
            final boolean rightAlignIds) {
        this._rightAlignIds = rightAlignIds;
        this._has_rightAlignIds = true;
    }

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

    /**
     * Sets the value of field 'showAnnotation'.
     * 
     * @param showAnnotation the value of field 'showAnnotation'.
     */
    public void setShowAnnotation(
            final boolean showAnnotation) {
        this._showAnnotation = showAnnotation;
        this._has_showAnnotation = true;
    }

    /**
     * Sets the value of field 'showBoxes'.
     * 
     * @param showBoxes the value of field 'showBoxes'.
     */
    public void setShowBoxes(
            final boolean showBoxes) {
        this._showBoxes = showBoxes;
        this._has_showBoxes = true;
    }

    /**
     * Sets the value of field 'showColourText'.
     * 
     * @param showColourText the value of field 'showColourText'.
     */
    public void setShowColourText(
            final boolean showColourText) {
        this._showColourText = showColourText;
        this._has_showColourText = true;
    }

    /**
     * Sets the value of field 'showConsensusHistogram'.
     * 
     * @param showConsensusHistogram the value of field
     * 'showConsensusHistogram'.
     */
    public void setShowConsensusHistogram(
            final boolean showConsensusHistogram) {
        this._showConsensusHistogram = showConsensusHistogram;
        this._has_showConsensusHistogram = true;
    }

    /**
     * Sets the value of field 'showDbRefTooltip'.
     * 
     * @param showDbRefTooltip the value of field 'showDbRefTooltip'
     */
    public void setShowDbRefTooltip(
            final boolean showDbRefTooltip) {
        this._showDbRefTooltip = showDbRefTooltip;
        this._has_showDbRefTooltip = true;
    }

    /**
     * Sets the value of field 'showFullId'.
     * 
     * @param showFullId the value of field 'showFullId'.
     */
    public void setShowFullId(
            final boolean showFullId) {
        this._showFullId = showFullId;
        this._has_showFullId = true;
    }

    /**
     * Sets the value of field 'showGroupConsensus'.
     * 
     * @param showGroupConsensus the value of field
     * 'showGroupConsensus'.
     */
    public void setShowGroupConsensus(
            final boolean showGroupConsensus) {
        this._showGroupConsensus = showGroupConsensus;
        this._has_showGroupConsensus = true;
    }

    /**
     * Sets the value of field 'showGroupConservation'.
     * 
     * @param showGroupConservation the value of field
     * 'showGroupConservation'.
     */
    public void setShowGroupConservation(
            final boolean showGroupConservation) {
        this._showGroupConservation = showGroupConservation;
        this._has_showGroupConservation = true;
    }

    /**
     * Sets the value of field 'showNPfeatureTooltip'.
     * 
     * @param showNPfeatureTooltip the value of field
     * 'showNPfeatureTooltip'.
     */
    public void setShowNPfeatureTooltip(
            final boolean showNPfeatureTooltip) {
        this._showNPfeatureTooltip = showNPfeatureTooltip;
        this._has_showNPfeatureTooltip = true;
    }

    /**
     * Sets the value of field 'showSequenceFeatures'.
     * 
     * @param showSequenceFeatures the value of field
     * 'showSequenceFeatures'.
     */
    public void setShowSequenceFeatures(
            final boolean showSequenceFeatures) {
        this._showSequenceFeatures = showSequenceFeatures;
        this._has_showSequenceFeatures = true;
    }

    /**
     * Sets the value of field 'showSequenceLogo'.
     * 
     * @param showSequenceLogo the value of field 'showSequenceLogo'
     */
    public void setShowSequenceLogo(
            final boolean showSequenceLogo) {
        this._showSequenceLogo = showSequenceLogo;
        this._has_showSequenceLogo = true;
    }

    /**
     * Sets the value of field 'showText'.
     * 
     * @param showText the value of field 'showText'.
     */
    public void setShowText(
            final boolean showText) {
        this._showText = showText;
        this._has_showText = true;
    }

    /**
     * Sets the value of field 'showUnconserved'.
     * 
     * @param showUnconserved the value of field 'showUnconserved'.
     */
    public void setShowUnconserved(
            final boolean showUnconserved) {
        this._showUnconserved = showUnconserved;
        this._has_showUnconserved = true;
    }

    /**
     * Sets the value of field 'startRes'.
     * 
     * @param startRes the value of field 'startRes'.
     */
    public void setStartRes(
            final int startRes) {
        this._startRes = startRes;
        this._has_startRes = true;
    }

    /**
     * Sets the value of field 'startSeq'.
     * 
     * @param startSeq the value of field 'startSeq'.
     */
    public void setStartSeq(
            final int startSeq) {
        this._startSeq = startSeq;
        this._has_startSeq = true;
    }

    /**
     * Sets the value of field 'textCol1'.
     * 
     * @param textCol1 the value of field 'textCol1'.
     */
    public void setTextCol1(
            final int textCol1) {
        this._textCol1 = textCol1;
        this._has_textCol1 = true;
    }

    /**
     * Sets the value of field 'textCol2'.
     * 
     * @param textCol2 the value of field 'textCol2'.
     */
    public void setTextCol2(
            final int textCol2) {
        this._textCol2 = textCol2;
        this._has_textCol2 = true;
    }

    /**
     * Sets the value of field 'textColThreshold'.
     * 
     * @param textColThreshold the value of field 'textColThreshold'
     */
    public void setTextColThreshold(
            final int textColThreshold) {
        this._textColThreshold = textColThreshold;
        this._has_textColThreshold = 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 'viewName'.
     * 
     * @param viewName the value of field 'viewName'.
     */
    public void setViewName(
            final java.lang.String viewName) {
        this._viewName = viewName;
    }

    /**
     * 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 'wrapAlignment'.
     * 
     * @param wrapAlignment the value of field 'wrapAlignment'.
     */
    public void setWrapAlignment(
            final boolean wrapAlignment) {
        this._wrapAlignment = wrapAlignment;
        this._has_wrapAlignment = 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 'ypos'.
     * 
     * @param ypos the value of field 'ypos'.
     */
    public void setYpos(
            final int ypos) {
        this._ypos = ypos;
        this._has_ypos = 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.Viewport
     */
    public static jalview.schemabinding.version2.Viewport unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.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);
    }

}