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    /* AlignMatchVector.java
     *
     * created: Sat Jun 17 2000
     *
     * This file is part of Artemis
     * 
     * Copyright (C) 2000,2001  Genome Research Limited
     * 
     * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
     *
    
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     * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/AlignMatchVector.java,v 1.3 2008-06-26 09:38:13 tjc Exp $
    
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     */
    
    package uk.ac.sanger.artemis;
    
    import uk.ac.sanger.artemis.util.FastVector;
    
    import java.util.Comparator;
    
    /**
     *  This class is a Vector of AlignMatch objects.
     *
     *  @author Kim Rutherford <kmr@sanger.ac.uk>
    
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     *  @version $Id: AlignMatchVector.java,v 1.3 2008-06-26 09:38:13 tjc Exp $
    
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     **/
    
    public class AlignMatchVector {
      /**
       *  Create a new (empty) AlignMatchVector object.
       **/
      public AlignMatchVector () {
    
      }
    
      /**
       *  Appends the given AlignMatch object to the vector if and only if it
       *  isn't already in the vector.
       **/
      public void addElement (AlignMatch item) {
        vector.add (item);
      }
      
      /**
       *  Appends the given AlignMatch object to the vector if and only if it
       *  isn't already in the vector.  (same as addElement ()).
       **/
      public void add (AlignMatch item) {
        addElement (item);
      }
      
      /**
       *  Performs the same function as Vector.elementAt ()
       **/
      public AlignMatch elementAt (int index) {
    
        return (AlignMatch) vector.get(index);
    
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      }
    
      /**
       *  Performs the same function as Vector.removeElement ()
       **/
      public boolean remove (AlignMatch item) {
        return vector.remove (item);
      }
    
      /**
       *  Return true if this object contains the given AlignMatch.
       **/
      public boolean contains (AlignMatch item) {
    
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        return vector.contains(item);
    
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      }
    
      /**
       *  Performs the same function as Vector.removeAllElements ()
       **/
      public void removeAllElements () {
    
        vector.clear ();
    
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      }
    
      /**
       *   Performs the same function as Vector.removeElement ()
       **/
      public int indexOf (AlignMatch item) {
        return vector.indexOf (item);
      }
    
      /**
       *  Performs the same function as Vector.size ()
       **/
      public int size () {
        return vector.size ();
      }
      
      /**
       *  Sort this vector.
       *  @param cmp The returned vector will be sorted with this Comparator.
       **/
      public void sort (final Comparator cmp) {
        vector = vector.sort (cmp);
      }
    
      /**
       *  Create a new AlignMatchVector with the same contents as this one.
       **/
      public Object clone () {
        final AlignMatchVector return_vector = new AlignMatchVector ();
        return_vector.vector = (FastVector) vector.clone ();
        return return_vector;
      }
    
      /**
       *  Storage for AlignMatch objects.
       **/
      private FastVector vector = new FastVector ();
    }