/*******************************************************************************
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 *
 * This file is part of Jalview.
 *
 * Jalview 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 3 of the License, or (at your option) any later version.
 *
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 *******************************************************************************/
/*
 * 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 Annotation.
 * 
 * @version $Revision$ $Date$
 */
public class Annotation implements java.io.Serializable {


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

    /**
     * Field _graph.
     */
    private boolean _graph;

    /**
     * keeps track of state for field: _graph
     */
    private boolean _has_graph;

    /**
     * Field _graphType.
     */
    private int _graphType;

    /**
     * keeps track of state for field: _graphType
     */
    private boolean _has_graphType;

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

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

    /**
     * Field _graphColour.
     */
    private int _graphColour;

    /**
     * keeps track of state for field: _graphColour
     */
    private boolean _has_graphColour;

    /**
     * Field _graphGroup.
     */
    private int _graphGroup;

    /**
     * keeps track of state for field: _graphGroup
     */
    private boolean _has_graphGroup;

    /**
     * height in pixels for the graph if this is a graph-type
     * annotation.
     */
    private int _graphHeight;

    /**
     * keeps track of state for field: _graphHeight
     */
    private boolean _has_graphHeight;

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

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

    /**
     * keeps track of state for field: _scoreOnly
     */
    private boolean _has_scoreOnly;

    /**
     * Field _score.
     */
    private double _score;

    /**
     * keeps track of state for field: _score
     */
    private boolean _has_score;

    /**
     * Field _visible.
     */
    private boolean _visible;

    /**
     * keeps track of state for field: _visible
     */
    private boolean _has_visible;

    /**
     * Field _centreColLabels.
     */
    private boolean _centreColLabels;

    /**
     * keeps track of state for field: _centreColLabels
     */
    private boolean _has_centreColLabels;

    /**
     * Field _scaleColLabels.
     */
    private boolean _scaleColLabels;

    /**
     * keeps track of state for field: _scaleColLabels
     */
    private boolean _has_scaleColLabels;

    /**
     * Field _showAllColLabels.
     */
    private boolean _showAllColLabels;

    /**
     * keeps track of state for field: _showAllColLabels
     */
    private boolean _has_showAllColLabels;

    /**
     * is an autocalculated annotation row
     */
    private boolean _autoCalculated = false;

    /**
     * keeps track of state for field: _autoCalculated
     */
    private boolean _has_autoCalculated;

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

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

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

    /**
     * Field _thresholdLine.
     */
    private jalview.schemabinding.version2.ThresholdLine _thresholdLine;


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

    public Annotation() {
        super();
        this._annotationElementList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vAnnotationElement
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAnnotationElement(
            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
    throws java.lang.IndexOutOfBoundsException {
        this._annotationElementList.addElement(vAnnotationElement);
    }

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

    /**
     */
    public void deleteAutoCalculated(
    ) {
        this._has_autoCalculated= false;
    }

    /**
     */
    public void deleteCentreColLabels(
    ) {
        this._has_centreColLabels= false;
    }

    /**
     */
    public void deleteGraph(
    ) {
        this._has_graph= false;
    }

    /**
     */
    public void deleteGraphColour(
    ) {
        this._has_graphColour= false;
    }

    /**
     */
    public void deleteGraphGroup(
    ) {
        this._has_graphGroup= false;
    }

    /**
     */
    public void deleteGraphHeight(
    ) {
        this._has_graphHeight= false;
    }

    /**
     */
    public void deleteGraphType(
    ) {
        this._has_graphType= false;
    }

    /**
     */
    public void deleteScaleColLabels(
    ) {
        this._has_scaleColLabels= false;
    }

    /**
     */
    public void deleteScore(
    ) {
        this._has_score= false;
    }

    /**
     */
    public void deleteScoreOnly(
    ) {
        this._has_scoreOnly= false;
    }

    /**
     */
    public void deleteShowAllColLabels(
    ) {
        this._has_showAllColLabels= false;
    }

    /**
     */
    public void deleteVisible(
    ) {
        this._has_visible= false;
    }

    /**
     * Method enumerateAnnotationElement.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.AnnotationElement elements
     */
    public java.util.Enumeration enumerateAnnotationElement(
    ) {
        return this._annotationElementList.elements();
    }

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

    /**
     * Method getAnnotationElement.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.AnnotationElement[] getAnnotationElement(
    ) {
        jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
        return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
    }

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

    /**
     * Returns the value of field 'autoCalculated'. The field
     * 'autoCalculated' has the following description: is an
     * autocalculated annotation row
     * 
     * @return the value of field 'AutoCalculated'.
     */
    public boolean getAutoCalculated(
    ) {
        return this._autoCalculated;
    }

    /**
     * Returns the value of field 'centreColLabels'.
     * 
     * @return the value of field 'CentreColLabels'.
     */
    public boolean getCentreColLabels(
    ) {
        return this._centreColLabels;
    }

    /**
     * Returns the value of field 'description'.
     * 
     * @return the value of field 'Description'.
     */
    public java.lang.String getDescription(
    ) {
        return this._description;
    }

    /**
     * Returns the value of field 'graph'.
     * 
     * @return the value of field 'Graph'.
     */
    public boolean getGraph(
    ) {
        return this._graph;
    }

    /**
     * Returns the value of field 'graphColour'.
     * 
     * @return the value of field 'GraphColour'.
     */
    public int getGraphColour(
    ) {
        return this._graphColour;
    }

    /**
     * Returns the value of field 'graphGroup'.
     * 
     * @return the value of field 'GraphGroup'.
     */
    public int getGraphGroup(
    ) {
        return this._graphGroup;
    }

    /**
     * Returns the value of field 'graphHeight'. The field
     * 'graphHeight' has the following description: height in
     * pixels for the graph if this is a graph-type annotation.
     * 
     * @return the value of field 'GraphHeight'.
     */
    public int getGraphHeight(
    ) {
        return this._graphHeight;
    }

    /**
     * Returns the value of field 'graphType'.
     * 
     * @return the value of field 'GraphType'.
     */
    public int getGraphType(
    ) {
        return this._graphType;
    }

    /**
     * Returns the value of field 'groupRef'.
     * 
     * @return the value of field 'GroupRef'.
     */
    public java.lang.String getGroupRef(
    ) {
        return this._groupRef;
    }

    /**
     * Returns the value of field 'id'.
     * 
     * @return the value of field 'Id'.
     */
    public java.lang.String getId(
    ) {
        return this._id;
    }

    /**
     * Returns the value of field 'label'.
     * 
     * @return the value of field 'Label'.
     */
    public java.lang.String getLabel(
    ) {
        return this._label;
    }

    /**
     * Returns the value of field 'scaleColLabels'.
     * 
     * @return the value of field 'ScaleColLabels'.
     */
    public boolean getScaleColLabels(
    ) {
        return this._scaleColLabels;
    }

    /**
     * Returns the value of field 'score'.
     * 
     * @return the value of field 'Score'.
     */
    public double getScore(
    ) {
        return this._score;
    }

    /**
     * Returns the value of field 'scoreOnly'.
     * 
     * @return the value of field 'ScoreOnly'.
     */
    public boolean getScoreOnly(
    ) {
        return this._scoreOnly;
    }

    /**
     * Returns the value of field 'sequenceRef'.
     * 
     * @return the value of field 'SequenceRef'.
     */
    public java.lang.String getSequenceRef(
    ) {
        return this._sequenceRef;
    }

    /**
     * Returns the value of field 'showAllColLabels'.
     * 
     * @return the value of field 'ShowAllColLabels'.
     */
    public boolean getShowAllColLabels(
    ) {
        return this._showAllColLabels;
    }

    /**
     * Returns the value of field 'thresholdLine'.
     * 
     * @return the value of field 'ThresholdLine'.
     */
    public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
    ) {
        return this._thresholdLine;
    }

    /**
     * Returns the value of field 'visible'.
     * 
     * @return the value of field 'Visible'.
     */
    public boolean getVisible(
    ) {
        return this._visible;
    }

    /**
     * Method hasAutoCalculated.
     * 
     * @return true if at least one AutoCalculated has been added
     */
    public boolean hasAutoCalculated(
    ) {
        return this._has_autoCalculated;
    }

    /**
     * Method hasCentreColLabels.
     * 
     * @return true if at least one CentreColLabels has been added
     */
    public boolean hasCentreColLabels(
    ) {
        return this._has_centreColLabels;
    }

    /**
     * Method hasGraph.
     * 
     * @return true if at least one Graph has been added
     */
    public boolean hasGraph(
    ) {
        return this._has_graph;
    }

    /**
     * Method hasGraphColour.
     * 
     * @return true if at least one GraphColour has been added
     */
    public boolean hasGraphColour(
    ) {
        return this._has_graphColour;
    }

    /**
     * Method hasGraphGroup.
     * 
     * @return true if at least one GraphGroup has been added
     */
    public boolean hasGraphGroup(
    ) {
        return this._has_graphGroup;
    }

    /**
     * Method hasGraphHeight.
     * 
     * @return true if at least one GraphHeight has been added
     */
    public boolean hasGraphHeight(
    ) {
        return this._has_graphHeight;
    }

    /**
     * Method hasGraphType.
     * 
     * @return true if at least one GraphType has been added
     */
    public boolean hasGraphType(
    ) {
        return this._has_graphType;
    }

    /**
     * Method hasScaleColLabels.
     * 
     * @return true if at least one ScaleColLabels has been added
     */
    public boolean hasScaleColLabels(
    ) {
        return this._has_scaleColLabels;
    }

    /**
     * Method hasScore.
     * 
     * @return true if at least one Score has been added
     */
    public boolean hasScore(
    ) {
        return this._has_score;
    }

    /**
     * Method hasScoreOnly.
     * 
     * @return true if at least one ScoreOnly has been added
     */
    public boolean hasScoreOnly(
    ) {
        return this._has_scoreOnly;
    }

    /**
     * Method hasShowAllColLabels.
     * 
     * @return true if at least one ShowAllColLabels has been added
     */
    public boolean hasShowAllColLabels(
    ) {
        return this._has_showAllColLabels;
    }

    /**
     * Method hasVisible.
     * 
     * @return true if at least one Visible has been added
     */
    public boolean hasVisible(
    ) {
        return this._has_visible;
    }

    /**
     * Returns the value of field 'autoCalculated'. The field
     * 'autoCalculated' has the following description: is an
     * autocalculated annotation row
     * 
     * @return the value of field 'AutoCalculated'.
     */
    public boolean isAutoCalculated(
    ) {
        return this._autoCalculated;
    }

    /**
     * Returns the value of field 'centreColLabels'.
     * 
     * @return the value of field 'CentreColLabels'.
     */
    public boolean isCentreColLabels(
    ) {
        return this._centreColLabels;
    }

    /**
     * Returns the value of field 'graph'.
     * 
     * @return the value of field 'Graph'.
     */
    public boolean isGraph(
    ) {
        return this._graph;
    }

    /**
     * Returns the value of field 'scaleColLabels'.
     * 
     * @return the value of field 'ScaleColLabels'.
     */
    public boolean isScaleColLabels(
    ) {
        return this._scaleColLabels;
    }

    /**
     * Returns the value of field 'scoreOnly'.
     * 
     * @return the value of field 'ScoreOnly'.
     */
    public boolean isScoreOnly(
    ) {
        return this._scoreOnly;
    }

    /**
     * Returns the value of field 'showAllColLabels'.
     * 
     * @return the value of field 'ShowAllColLabels'.
     */
    public boolean isShowAllColLabels(
    ) {
        return this._showAllColLabels;
    }

    /**
     * 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 'visible'.
     * 
     * @return the value of field 'Visible'.
     */
    public boolean isVisible(
    ) {
        return this._visible;
    }

    /**
     * 
     * 
     * @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 removeAllAnnotationElement(
    ) {
        this._annotationElementList.clear();
    }

    /**
     * Method removeAnnotationElement.
     * 
     * @param vAnnotationElement
     * @return true if the object was removed from the collection.
     */
    public boolean removeAnnotationElement(
            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
        boolean removed = _annotationElementList.remove(vAnnotationElement);
        return removed;
    }

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

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

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

    /**
     * Sets the value of field 'autoCalculated'. The field
     * 'autoCalculated' has the following description: is an
     * autocalculated annotation row
     * 
     * @param autoCalculated the value of field 'autoCalculated'.
     */
    public void setAutoCalculated(
            final boolean autoCalculated) {
        this._autoCalculated = autoCalculated;
        this._has_autoCalculated = true;
    }

    /**
     * Sets the value of field 'centreColLabels'.
     * 
     * @param centreColLabels the value of field 'centreColLabels'.
     */
    public void setCentreColLabels(
            final boolean centreColLabels) {
        this._centreColLabels = centreColLabels;
        this._has_centreColLabels = true;
    }

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

    /**
     * Sets the value of field 'graph'.
     * 
     * @param graph the value of field 'graph'.
     */
    public void setGraph(
            final boolean graph) {
        this._graph = graph;
        this._has_graph = true;
    }

    /**
     * Sets the value of field 'graphColour'.
     * 
     * @param graphColour the value of field 'graphColour'.
     */
    public void setGraphColour(
            final int graphColour) {
        this._graphColour = graphColour;
        this._has_graphColour = true;
    }

    /**
     * Sets the value of field 'graphGroup'.
     * 
     * @param graphGroup the value of field 'graphGroup'.
     */
    public void setGraphGroup(
            final int graphGroup) {
        this._graphGroup = graphGroup;
        this._has_graphGroup = true;
    }

    /**
     * Sets the value of field 'graphHeight'. The field
     * 'graphHeight' has the following description: height in
     * pixels for the graph if this is a graph-type annotation.
     * 
     * @param graphHeight the value of field 'graphHeight'.
     */
    public void setGraphHeight(
            final int graphHeight) {
        this._graphHeight = graphHeight;
        this._has_graphHeight = true;
    }

    /**
     * Sets the value of field 'graphType'.
     * 
     * @param graphType the value of field 'graphType'.
     */
    public void setGraphType(
            final int graphType) {
        this._graphType = graphType;
        this._has_graphType = true;
    }

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

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

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

    /**
     * Sets the value of field 'scaleColLabels'.
     * 
     * @param scaleColLabels the value of field 'scaleColLabels'.
     */
    public void setScaleColLabels(
            final boolean scaleColLabels) {
        this._scaleColLabels = scaleColLabels;
        this._has_scaleColLabels = true;
    }

    /**
     * Sets the value of field 'score'.
     * 
     * @param score the value of field 'score'.
     */
    public void setScore(
            final double score) {
        this._score = score;
        this._has_score = true;
    }

    /**
     * Sets the value of field 'scoreOnly'.
     * 
     * @param scoreOnly the value of field 'scoreOnly'.
     */
    public void setScoreOnly(
            final boolean scoreOnly) {
        this._scoreOnly = scoreOnly;
        this._has_scoreOnly = true;
    }

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

    /**
     * Sets the value of field 'showAllColLabels'.
     * 
     * @param showAllColLabels the value of field 'showAllColLabels'
     */
    public void setShowAllColLabels(
            final boolean showAllColLabels) {
        this._showAllColLabels = showAllColLabels;
        this._has_showAllColLabels = true;
    }

    /**
     * Sets the value of field 'thresholdLine'.
     * 
     * @param thresholdLine the value of field 'thresholdLine'.
     */
    public void setThresholdLine(
            final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
        this._thresholdLine = thresholdLine;
    }

    /**
     * Sets the value of field 'visible'.
     * 
     * @param visible the value of field 'visible'.
     */
    public void setVisible(
            final boolean visible) {
        this._visible = visible;
        this._has_visible = 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.Annotation
     */
    public static jalview.schemabinding.version2.Annotation unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.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);
    }

}