extended Colour element with additional optional attributes for graduated colour

[jalview.git] / src / jalview / binding / Viewport.java

/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.binding;

  //---------------------------------/
 //- 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 _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 _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 _showAnnotation.
     */
    private boolean _showAnnotation;

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

    /**
     * Field _showConservation.
     */
    private boolean _showConservation;

    /**
     * keeps track of state for field: _showConservation
     */
    private boolean _has_showConservation;

    /**
     * Field _showQuality.
     */
    private boolean _showQuality;

    /**
     * keeps track of state for field: _showQuality
     */
    private boolean _has_showQuality;

    /**
     * Field _showIdentity.
     */
    private boolean _showIdentity;

    /**
     * keeps track of state for field: _showIdentity
     */
    private boolean _has_showIdentity;

    /**
     * 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 _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 _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;


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

    public Viewport() {
        super();
    }


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

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

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

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

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

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

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

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

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

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

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

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

    /**
     */
    public void deleteShowConservation(
    ) {
        this._has_showConservation= false;
    }

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

    /**
     */
    public void deleteShowIdentity(
    ) {
        this._has_showIdentity= false;
    }

    /**
     */
    public void deleteShowQuality(
    ) {
        this._has_showQuality= false;
    }

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

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

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

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

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

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

    /**
     * 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 '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 'showConservation'.
     * 
     * @return the value of field 'ShowConservation'.
     */
    public boolean getShowConservation(
    ) {
        return this._showConservation;
    }

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

    /**
     * Returns the value of field 'showIdentity'.
     * 
     * @return the value of field 'ShowIdentity'.
     */
    public boolean getShowIdentity(
    ) {
        return this._showIdentity;
    }

    /**
     * Returns the value of field 'showQuality'.
     * 
     * @return the value of field 'ShowQuality'.
     */
    public boolean getShowQuality(
    ) {
        return this._showQuality;
    }

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

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

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

    /**
     * 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 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 hasShowConservation.
     * 
     * @return true if at least one ShowConservation has been added
     */
    public boolean hasShowConservation(
    ) {
        return this._has_showConservation;
    }

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

    /**
     * Method hasShowIdentity.
     * 
     * @return true if at least one ShowIdentity has been added
     */
    public boolean hasShowIdentity(
    ) {
        return this._has_showIdentity;
    }

    /**
     * Method hasShowQuality.
     * 
     * @return true if at least one ShowQuality has been added
     */
    public boolean hasShowQuality(
    ) {
        return this._has_showQuality;
    }

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

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

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

    /**
     * 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 '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 'showConservation'.
     * 
     * @return the value of field 'ShowConservation'.
     */
    public boolean isShowConservation(
    ) {
        return this._showConservation;
    }

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

    /**
     * Returns the value of field 'showIdentity'.
     * 
     * @return the value of field 'ShowIdentity'.
     */
    public boolean isShowIdentity(
    ) {
        return this._showIdentity;
    }

    /**
     * Returns the value of field 'showQuality'.
     * 
     * @return the value of field 'ShowQuality'.
     */
    public boolean isShowQuality(
    ) {
        return this._showQuality;
    }

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

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

    /**
     * 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);
    }

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

    /**
     * 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 '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 '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 '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 '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 'showConservation'.
     * 
     * @param showConservation the value of field 'showConservation'
     */
    public void setShowConservation(
            final boolean showConservation) {
        this._showConservation = showConservation;
        this._has_showConservation = 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 'showIdentity'.
     * 
     * @param showIdentity the value of field 'showIdentity'.
     */
    public void setShowIdentity(
            final boolean showIdentity) {
        this._showIdentity = showIdentity;
        this._has_showIdentity = true;
    }

    /**
     * Sets the value of field 'showQuality'.
     * 
     * @param showQuality the value of field 'showQuality'.
     */
    public void setShowQuality(
            final boolean showQuality) {
        this._showQuality = showQuality;
        this._has_showQuality = 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 '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 '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 '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 '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.binding.Viewport
     */
    public static jalview.binding.Viewport unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.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);
    }

}