/*
 * 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;

/**
 * Reference to a viewer showing RNA structure
 *  for this sequence. Schema supports one viewer showing multiple
 *  annotations for multiple sequences, though currently only one
 *  annotation for one sequence (gapped or trimmed) is used
 *  
 * 
 * @version $Revision$ $Date$
 */
public class RnaViewer implements java.io.Serializable {


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

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

    /**
     * An id unique to the RNA viewer panel
     *  
     */
    private java.lang.String _viewId;

    /**
     * horizontal position of split pane divider
     *  
     */
    private int _dividerLocation;

    /**
     * keeps track of state for field: _dividerLocation
     */
    private boolean _has_dividerLocation;

    /**
     * Index of the selected structure in the
     *  viewer panel
     *  
     */
    private int _selectedRna;

    /**
     * keeps track of state for field: _selectedRna
     */
    private boolean _has_selectedRna;

    /**
     * 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 _secondaryStructureList.
     */
    private java.util.Vector _secondaryStructureList;


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

    public RnaViewer() {
        super();
        this._secondaryStructureList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vSecondaryStructure
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSecondaryStructure(
            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
    throws java.lang.IndexOutOfBoundsException {
        this._secondaryStructureList.addElement(vSecondaryStructure);
    }

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

    /**
     */
    public void deleteDividerLocation(
    ) {
        this._has_dividerLocation= false;
    }

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

    /**
     */
    public void deleteSelectedRna(
    ) {
        this._has_selectedRna= false;
    }

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

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

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

    /**
     * Method enumerateSecondaryStructure.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.SecondaryStructure elements
     */
    public java.util.Enumeration enumerateSecondaryStructure(
    ) {
        return this._secondaryStructureList.elements();
    }

    /**
     * Returns the value of field 'dividerLocation'. The field
     * 'dividerLocation' has the following description: horizontal
     * position of split pane divider
     *  
     * 
     * @return the value of field 'DividerLocation'.
     */
    public int getDividerLocation(
    ) {
        return this._dividerLocation;
    }

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

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

    /**
     * Method getSecondaryStructure.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.SecondaryStructure[] getSecondaryStructure(
    ) {
        jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
        return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList.toArray(array);
    }

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

    /**
     * Returns the value of field 'selectedRna'. The field
     * 'selectedRna' has the following description: Index of the
     * selected structure in the
     *  viewer panel
     *  
     * 
     * @return the value of field 'SelectedRna'.
     */
    public int getSelectedRna(
    ) {
        return this._selectedRna;
    }

    /**
     * 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 'viewId'. The field 'viewId' has
     * the following description: An id unique to the RNA viewer
     * panel
     *  
     * 
     * @return the value of field 'ViewId'.
     */
    public java.lang.String getViewId(
    ) {
        return this._viewId;
    }

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

    /**
     * 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 hasDividerLocation.
     * 
     * @return true if at least one DividerLocation has been added
     */
    public boolean hasDividerLocation(
    ) {
        return this._has_dividerLocation;
    }

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

    /**
     * Method hasSelectedRna.
     * 
     * @return true if at least one SelectedRna has been added
     */
    public boolean hasSelectedRna(
    ) {
        return this._has_selectedRna;
    }

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

    /**
     * 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;
    }

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

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

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

    /**
     */
    public void removeAllSecondaryStructure(
    ) {
        this._secondaryStructureList.clear();
    }

    /**
     * Method removeSecondaryStructure.
     * 
     * @param vSecondaryStructure
     * @return true if the object was removed from the collection.
     */
    public boolean removeSecondaryStructure(
            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) {
        boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
        return removed;
    }

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

    /**
     * Sets the value of field 'dividerLocation'. The field
     * 'dividerLocation' has the following description: horizontal
     * position of split pane divider
     *  
     * 
     * @param dividerLocation the value of field 'dividerLocation'.
     */
    public void setDividerLocation(
            final int dividerLocation) {
        this._dividerLocation = dividerLocation;
        this._has_dividerLocation = 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 vSecondaryStructure
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setSecondaryStructure(
            final int index,
            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._secondaryStructureList.size()) {
            throw new IndexOutOfBoundsException("setSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
        }
        
        this._secondaryStructureList.set(index, vSecondaryStructure);
    }

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

    /**
     * Sets the value of field 'selectedRna'. The field
     * 'selectedRna' has the following description: Index of the
     * selected structure in the
     *  viewer panel
     *  
     * 
     * @param selectedRna the value of field 'selectedRna'.
     */
    public void setSelectedRna(
            final int selectedRna) {
        this._selectedRna = selectedRna;
        this._has_selectedRna = 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 'viewId'. The field 'viewId' has the
     * following description: An id unique to the RNA viewer panel
     *  
     * 
     * @param viewId the value of field 'viewId'.
     */
    public void setViewId(
            final java.lang.String viewId) {
        this._viewId = viewId;
    }

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

}