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


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

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

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


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

    public AlcodonFrame() {
        super();
        this._alcodonList = new java.util.Vector();
        this._alcodMapList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vAlcodMap
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAlcodMap(
            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
    throws java.lang.IndexOutOfBoundsException {
        this._alcodMapList.addElement(vAlcodMap);
    }

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

    /**
     * 
     * 
     * @param vAlcodon
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAlcodon(
            final jalview.schemabinding.version2.Alcodon vAlcodon)
    throws java.lang.IndexOutOfBoundsException {
        this._alcodonList.addElement(vAlcodon);
    }

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

    /**
     * Method enumerateAlcodMap.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.AlcodMap elements
     */
    public java.util.Enumeration enumerateAlcodMap(
    ) {
        return this._alcodMapList.elements();
    }

    /**
     * Method enumerateAlcodon.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.Alcodon elements
     */
    public java.util.Enumeration enumerateAlcodon(
    ) {
        return this._alcodonList.elements();
    }

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

    /**
     * Method getAlcodMap.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.AlcodMap[] getAlcodMap(
    ) {
        jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
        return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);
    }

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

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

    /**
     * Method getAlcodon.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.Alcodon[] getAlcodon(
    ) {
        jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
        return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
    }

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

    /**
     * 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);
    }

    /**
     * Method removeAlcodMap.
     * 
     * @param vAlcodMap
     * @return true if the object was removed from the collection.
     */
    public boolean removeAlcodMap(
            final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
        boolean removed = _alcodMapList.remove(vAlcodMap);
        return removed;
    }

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

    /**
     * Method removeAlcodon.
     * 
     * @param vAlcodon
     * @return true if the object was removed from the collection.
     */
    public boolean removeAlcodon(
            final jalview.schemabinding.version2.Alcodon vAlcodon) {
        boolean removed = _alcodonList.remove(vAlcodon);
        return removed;
    }

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

    /**
     */
    public void removeAllAlcodMap(
    ) {
        this._alcodMapList.clear();
    }

    /**
     */
    public void removeAllAlcodon(
    ) {
        this._alcodonList.clear();
    }

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

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

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

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

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

}