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


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

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

    /**
     * id attribute of Annotation in
     *  vamsasModel for
     *  the secondary structure annotation shown
     *  in the viewer
     *  
     */
    private java.lang.String _annotationId;

    /**
     * if true the RNA structure is shown with gaps, if false
     * without
     *  
     */
    private boolean _gapped;

    /**
     * keeps track of state for field: _gapped
     */
    private boolean _has_gapped;

    /**
     * name of the project jar entry that holds
     *  the VARNA viewer state for the structure
     *  
     */
    private java.lang.String _viewerState;


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

    public SecondaryStructure() {
        super();
    }


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

    /**
     */
    public void deleteGapped(
    ) {
        this._has_gapped= false;
    }

    /**
     * Returns the value of field 'annotationId'. The field
     * 'annotationId' has the following description: id attribute
     * of Annotation in
     *  vamsasModel for
     *  the secondary structure annotation shown
     *  in the viewer
     *  
     * 
     * @return the value of field 'AnnotationId'.
     */
    public java.lang.String getAnnotationId(
    ) {
        return this._annotationId;
    }

    /**
     * Returns the value of field 'gapped'. The field 'gapped' has
     * the following description: if true the RNA structure is
     * shown with gaps, if false without
     *  
     * 
     * @return the value of field 'Gapped'.
     */
    public boolean getGapped(
    ) {
        return this._gapped;
    }

    /**
     * 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 'viewerState'. The field
     * 'viewerState' has the following description: name of the
     * project jar entry that holds
     *  the VARNA viewer state for the structure
     *  
     * 
     * @return the value of field 'ViewerState'.
     */
    public java.lang.String getViewerState(
    ) {
        return this._viewerState;
    }

    /**
     * Method hasGapped.
     * 
     * @return true if at least one Gapped has been added
     */
    public boolean hasGapped(
    ) {
        return this._has_gapped;
    }

    /**
     * Returns the value of field 'gapped'. The field 'gapped' has
     * the following description: if true the RNA structure is
     * shown with gaps, if false without
     *  
     * 
     * @return the value of field 'Gapped'.
     */
    public boolean isGapped(
    ) {
        return this._gapped;
    }

    /**
     * Method isValid.
     * 
     * @return true if this object is valid according to the schema
     */
    public boolean isValid(
    ) {
        try {
            validate();
        } catch (org.exolab.castor.xml.ValidationException vex) {
            return false;
        }
        return true;
    }

    /**
     * 
     * 
     * @param out
     * @throws org.exolab.castor.xml.MarshalException if object is
     * null or if any SAXException is thrown during marshaling
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     */
    public void marshal(
            final java.io.Writer out)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, out);
    }

    /**
     * 
     * 
     * @param handler
     * @throws java.io.IOException if an IOException occurs during
     * marshaling
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     * @throws org.exolab.castor.xml.MarshalException if object is
     * null or if any SAXException is thrown during marshaling
     */
    public void marshal(
            final org.xml.sax.ContentHandler handler)
    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, handler);
    }

    /**
     * Sets the value of field 'annotationId'. The field
     * 'annotationId' has the following description: id attribute
     * of Annotation in
     *  vamsasModel for
     *  the secondary structure annotation shown
     *  in the viewer
     *  
     * 
     * @param annotationId the value of field 'annotationId'.
     */
    public void setAnnotationId(
            final java.lang.String annotationId) {
        this._annotationId = annotationId;
    }

    /**
     * Sets the value of field 'gapped'. The field 'gapped' has the
     * following description: if true the RNA structure is shown
     * with gaps, if false without
     *  
     * 
     * @param gapped the value of field 'gapped'.
     */
    public void setGapped(
            final boolean gapped) {
        this._gapped = gapped;
        this._has_gapped = 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 'viewerState'. The field
     * 'viewerState' has the following description: name of the
     * project jar entry that holds
     *  the VARNA viewer state for the structure
     *  
     * 
     * @param viewerState the value of field 'viewerState'.
     */
    public void setViewerState(
            final java.lang.String viewerState) {
        this._viewerState = viewerState;
    }

    /**
     * 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.SecondaryStructure
     */
    public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.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);
    }

}