/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 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.schemabinding.version2;

  //---------------------------------/
 //- Imported classes and packages -/
//---------------------------------/

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

/**
 * Class Sequence.
 * 
 * @version $Revision$ $Date$
 */
public class Sequence extends jalview.schemabinding.version2.SequenceType 
implements java.io.Serializable
{


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

    /**
     * dataset sequence id for this sequence. Will be created as
     * union of sequences.
     *  
     */
    private java.lang.String _dsseqid;

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


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

    public Sequence() {
        super();
        this._DBRefList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vDBRef
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDBRef(
            final jalview.schemabinding.version2.DBRef vDBRef)
    throws java.lang.IndexOutOfBoundsException {
        this._DBRefList.addElement(vDBRef);
    }

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

    /**
     * Method enumerateDBRef.
     * 
     * @return an Enumeration over all
     * jalview.schemabinding.version2.DBRef elements
     */
    public java.util.Enumeration enumerateDBRef(
    ) {
        return this._DBRefList.elements();
    }

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

    /**
     * Method getDBRef.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.DBRef[] getDBRef(
    ) {
        jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
        return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
    }

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

    /**
     * Returns the value of field 'dsseqid'. The field 'dsseqid'
     * has the following description: dataset sequence id for this
     * sequence. Will be created as union of sequences.
     *  
     * 
     * @return the value of field 'Dsseqid'.
     */
    public java.lang.String getDsseqid(
    ) {
        return this._dsseqid;
    }

    /**
     * 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 removeAllDBRef(
    ) {
        this._DBRefList.clear();
    }

    /**
     * Method removeDBRef.
     * 
     * @param vDBRef
     * @return true if the object was removed from the collection.
     */
    public boolean removeDBRef(
            final jalview.schemabinding.version2.DBRef vDBRef) {
        boolean removed = _DBRefList.remove(vDBRef);
        return removed;
    }

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

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

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

    /**
     * Sets the value of field 'dsseqid'. The field 'dsseqid' has
     * the following description: dataset sequence id for this
     * sequence. Will be created as union of sequences.
     *  
     * 
     * @param dsseqid the value of field 'dsseqid'.
     */
    public void setDsseqid(
            final java.lang.String dsseqid) {
        this._dsseqid = dsseqid;
    }

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

}