/*
 * This class was automatically generated with
 * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
 * Schema.
 * $Id$
 */
/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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;

import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
import org.exolab.castor.xml.ValidationException;

import org.xml.sax.ContentHandler;

//---------------------------------/
//- Imported classes and packages -/
//---------------------------------/
import java.io.IOException;
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;

import java.util.Enumeration;
import java.util.Vector;


/**
 * Class SequenceSet.
 *
 * @version $Revision$ $Date$
 */
public class SequenceSet implements java.io.Serializable {
    //--------------------------/
    //- Class/Member Variables -/
    //--------------------------/

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

    /**
     * Field _aligned
     */
    private boolean _aligned;

    /**
     * keeps track of state for field: _aligned
     */
    private boolean _has_aligned;

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

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

    //----------------/
    //- Constructors -/
    //----------------/
    public SequenceSet() {
        super();
        _sequenceList = new Vector();
        _annotationList = new Vector();
    }
     //-- jalview.binding.SequenceSet()
 //-----------/

    public void addAnnotation(jalview.binding.Annotation vAnnotation)
        throws java.lang.IndexOutOfBoundsException {
        _annotationList.addElement(vAnnotation);
    }
     //-- void addAnnotation(jalview.binding.Annotation)

    /**
     * Method addAnnotation
     *
     *
     *
     * @param index
     * @param vAnnotation
     */
    public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)
        throws java.lang.IndexOutOfBoundsException {
        _annotationList.insertElementAt(vAnnotation, index);
    }
     //-- void addAnnotation(int, jalview.binding.Annotation)

    /**
     * Method addSequence
     *
     *
     *
     * @param vSequence
     */
    public void addSequence(jalview.binding.Sequence vSequence)
        throws java.lang.IndexOutOfBoundsException {
        _sequenceList.addElement(vSequence);
    }
     //-- void addSequence(jalview.binding.Sequence)

    /**
     * Method addSequence
     *
     *
     *
     * @param index
     * @param vSequence
     */
    public void addSequence(int index, jalview.binding.Sequence vSequence)
        throws java.lang.IndexOutOfBoundsException {
        _sequenceList.insertElementAt(vSequence, index);
    }
     //-- void addSequence(int, jalview.binding.Sequence)

    /**
     * Method deleteAligned
     *
     */
    public void deleteAligned() {
        this._has_aligned = false;
    }
     //-- void deleteAligned()

    /**
     * Method enumerateAnnotation
     *
     *
     *
     * @return Enumeration
     */
    public java.util.Enumeration enumerateAnnotation() {
        return _annotationList.elements();
    }
     //-- java.util.Enumeration enumerateAnnotation()

    /**
     * Method enumerateSequence
     *
     *
     *
     * @return Enumeration
     */
    public java.util.Enumeration enumerateSequence() {
        return _sequenceList.elements();
    }
     //-- java.util.Enumeration enumerateSequence()

    /**
     * Returns the value of field 'aligned'.
     *
     * @return boolean
     * @return the value of field 'aligned'.
     */
    public boolean getAligned() {
        return this._aligned;
    }
     //-- boolean getAligned()

    /**
     * Method getAnnotation
     *
     *
     *
     * @param index
     * @return Annotation
     */
    public jalview.binding.Annotation getAnnotation(int index)
        throws java.lang.IndexOutOfBoundsException {
        //-- check bounds for index
        if ((index < 0) || (index > _annotationList.size())) {
            throw new IndexOutOfBoundsException();
        }

        return (jalview.binding.Annotation) _annotationList.elementAt(index);
    }
     //-- jalview.binding.Annotation getAnnotation(int)

    /**
     * Method getAnnotation
     *
     *
     *
     * @return Annotation
     */
    public jalview.binding.Annotation[] getAnnotation() {
        int size = _annotationList.size();
        jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];

        for (int index = 0; index < size; index++) {
            mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
        }

        return mArray;
    }
     //-- jalview.binding.Annotation[] getAnnotation()

    /**
     * Method getAnnotationCount
     *
     *
     *
     * @return int
     */
    public int getAnnotationCount() {
        return _annotationList.size();
    }
     //-- int getAnnotationCount()

    /**
     * Returns the value of field 'gapChar'.
     *
     * @return String
     * @return the value of field 'gapChar'.
     */
    public java.lang.String getGapChar() {
        return this._gapChar;
    }
     //-- java.lang.String getGapChar()

    /**
     * Method getSequence
     *
     *
     *
     * @param index
     * @return Sequence
     */
    public jalview.binding.Sequence getSequence(int index)
        throws java.lang.IndexOutOfBoundsException {
        //-- check bounds for index
        if ((index < 0) || (index > _sequenceList.size())) {
            throw new IndexOutOfBoundsException();
        }

        return (jalview.binding.Sequence) _sequenceList.elementAt(index);
    }
     //-- jalview.binding.Sequence getSequence(int)

    /**
     * Method getSequence
     *
     *
     *
     * @return Sequence
     */
    public jalview.binding.Sequence[] getSequence() {
        int size = _sequenceList.size();
        jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];

        for (int index = 0; index < size; index++) {
            mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
        }

        return mArray;
    }
     //-- jalview.binding.Sequence[] getSequence()

    /**
     * Method getSequenceCount
     *
     *
     *
     * @return int
     */
    public int getSequenceCount() {
        return _sequenceList.size();
    }
     //-- int getSequenceCount()

    /**
     * Method hasAligned
     *
     *
     *
     * @return boolean
     */
    public boolean hasAligned() {
        return this._has_aligned;
    }
     //-- boolean hasAligned()

    /**
     * Method isValid
     *
     *
     *
     * @return boolean
     */
    public boolean isValid() {
        try {
            validate();
        } catch (org.exolab.castor.xml.ValidationException vex) {
            return false;
        }

        return true;
    }
     //-- boolean isValid()

    /**
     * Method marshal
     *
     *
     *
     * @param out
     */
    public void marshal(java.io.Writer out)
        throws org.exolab.castor.xml.MarshalException, 
            org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, out);
    }
     //-- void marshal(java.io.Writer)

    /**
     * Method marshal
     *
     *
     *
     * @param handler
     */
    public void marshal(org.xml.sax.ContentHandler handler)
        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
            org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, handler);
    }
     //-- void marshal(org.xml.sax.ContentHandler)

    /**
     * Method removeAllAnnotation
     *
     */
    public void removeAllAnnotation() {
        _annotationList.removeAllElements();
    }
     //-- void removeAllAnnotation()

    /**
     * Method removeAllSequence
     *
     */
    public void removeAllSequence() {
        _sequenceList.removeAllElements();
    }
     //-- void removeAllSequence()

    /**
     * Method removeAnnotation
     *
     *
     *
     * @param index
     * @return Annotation
     */
    public jalview.binding.Annotation removeAnnotation(int index) {
        java.lang.Object obj = _annotationList.elementAt(index);
        _annotationList.removeElementAt(index);

        return (jalview.binding.Annotation) obj;
    }
     //-- jalview.binding.Annotation removeAnnotation(int)

    /**
     * Method removeSequence
     *
     *
     *
     * @param index
     * @return Sequence
     */
    public jalview.binding.Sequence removeSequence(int index) {
        java.lang.Object obj = _sequenceList.elementAt(index);
        _sequenceList.removeElementAt(index);

        return (jalview.binding.Sequence) obj;
    }
     //-- jalview.binding.Sequence removeSequence(int)

    /**
     * Sets the value of field 'aligned'.
     *
     * @param aligned the value of field 'aligned'.
     */
    public void setAligned(boolean aligned) {
        this._aligned = aligned;
        this._has_aligned = true;
    }
     //-- void setAligned(boolean)

    /**
     * Method setAnnotation
     *
     *
     *
     * @param index
     * @param vAnnotation
     */
    public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)
        throws java.lang.IndexOutOfBoundsException {
        //-- check bounds for index
        if ((index < 0) || (index > _annotationList.size())) {
            throw new IndexOutOfBoundsException();
        }

        _annotationList.setElementAt(vAnnotation, index);
    }
     //-- void setAnnotation(int, jalview.binding.Annotation)

    /**
     * Method setAnnotation
     *
     *
     *
     * @param annotationArray
     */
    public void setAnnotation(jalview.binding.Annotation[] annotationArray) {
        //-- copy array
        _annotationList.removeAllElements();

        for (int i = 0; i < annotationArray.length; i++) {
            _annotationList.addElement(annotationArray[i]);
        }
    }
     //-- void setAnnotation(jalview.binding.Annotation)

    /**
     * Sets the value of field 'gapChar'.
     *
     * @param gapChar the value of field 'gapChar'.
     */
    public void setGapChar(java.lang.String gapChar) {
        this._gapChar = gapChar;
    }
     //-- void setGapChar(java.lang.String)

    /**
     * Method setSequence
     *
     *
     *
     * @param index
     * @param vSequence
     */
    public void setSequence(int index, jalview.binding.Sequence vSequence)
        throws java.lang.IndexOutOfBoundsException {
        //-- check bounds for index
        if ((index < 0) || (index > _sequenceList.size())) {
            throw new IndexOutOfBoundsException();
        }

        _sequenceList.setElementAt(vSequence, index);
    }
     //-- void setSequence(int, jalview.binding.Sequence)

    /**
     * Method setSequence
     *
     *
     *
     * @param sequenceArray
     */
    public void setSequence(jalview.binding.Sequence[] sequenceArray) {
        //-- copy array
        _sequenceList.removeAllElements();

        for (int i = 0; i < sequenceArray.length; i++) {
            _sequenceList.addElement(sequenceArray[i]);
        }
    }
     //-- void setSequence(jalview.binding.Sequence)

    /**
     * Method unmarshal
     *
     *
     *
     * @param reader
     * @return Object
     */
    public static java.lang.Object unmarshal(java.io.Reader reader)
        throws org.exolab.castor.xml.MarshalException, 
            org.exolab.castor.xml.ValidationException {
        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,
            reader);
    }
     //-- java.lang.Object unmarshal(java.io.Reader)

    /**
     * Method validate
     *
     */
    public void validate() throws org.exolab.castor.xml.ValidationException {
        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
        validator.validate(this);
    }
     //-- void validate()
}