BlastM8ComparisonData.java

/* BlastM8ComparisonData.java
 *
 * created: Tue Apr 30 2002
 *
 * This file is part of Artemis
 * 
 * Copyright (C) 2002  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.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/BlastM8ComparisonData.java,v 1.2 2007-02-27 10:24:32 tjc Exp $
 */

package uk.ac.sanger.artemis;

import uk.ac.sanger.artemis.util.LinePushBackReader;

import java.io.*;
import java.util.StringTokenizer;
import java.util.Vector;

/**
 *  This class implements the ComparisonData interface for blastall -m 8
 *  output.
 *
 *  @author Kim Rutherford <kmr@sanger.ac.uk>
 *  @version $Id: BlastM8ComparisonData.java,v 1.2 2007-02-27 10:24:32 tjc Exp $
 **/

public class BlastM8ComparisonData extends SimpleComparisonData {
  /**
   *  Create a new BlastM8ComparisonData by reading from the given
   *  LinePushBackReader.
   **/
  public BlastM8ComparisonData (final LinePushBackReader stream)
      throws IOException {
    super (stream);
  }

  /**
   *  Create a new, empty instance of BlastM8ComparisonData.
   **/
  public BlastM8ComparisonData () {
    
  }

  /**
   *  Returns a new, empty instance of this type of object;
   **/
  protected SimpleComparisonData getNewSimpleComparisonData () {
    return new BlastM8ComparisonData ();
  }


  /**
   *  Make an AlignMatch object from the given String.
   **/
  private static AlignMatch makeMatchFromStringStatic (String line)