[Biojava-l] FramedFeature interface

[Schreiber, Mark]

Hi -

Below is a work up for a possible FramedFeature interface

Any comments?

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

package org.biojava.bio.seq;

import java.io.*;

import org.biojava.bio.symbol.*;

/**
 * Title:         FramedFeature<p>
 * Description:  An feature that includes the concept of frame.<p>
 * By extending stranded
 * Copyright:    Copyright (c) 2001<p>
 * @author Mark Schreiber
 * @version 1.0
 */

public interface FramedFeature extends StrandedFeature {

  public static ReadingFrame FORWARD_1 = new ReadingFrame("FORWARD_1",+1);
  public static ReadingFrame FORWARD_2 = new ReadingFrame("FORWARD_2",+2);
  public static ReadingFrame FORWARD_3 = new ReadingFrame("FORWARD_3",+3);
  public static ReadingFrame REVERSE_1 = new ReadingFrame("REVERSE_1",-1);
  public static ReadingFrame REVERSE_2 = new ReadingFrame("REVERSE_2",-2);
  public static ReadingFrame REVERSE_3 = new ReadingFrame("REVERSE_3",-3);

  /**
   * return the reading frame of the feature.
   */
  ReadingFrame getReadingFrame();

  /**
   * This method should be implemented such that a feature on the reverse
strand  is reverse
   * complemented
   */
  SymbolList getSymbols();

  /**
   * @return the Strand that the feature is found on
   */
  Strand getStrand();

  /**
   * Note that the template does not extend StrandedFeature.Template,
   * This is because the concept of strand is encapsulated in the
ReadingFrame
   */
  public static class Template extends Feature.Template{
    public static ReadingFrame readingFrame;
  }

  public static class ReadingFrame implements Serializable{
    private final String text;
    private final int value;
    private final Strand strand;

    private ReadingFrame(String text, int value){
      this.text = text;
      this.value = value;
      if(value > 0) this.strand = StrandedFeature.POSITIVE;
      else this.strand = StrandedFeature.NEGATIVE;
    }

    public String toString(){
      return text;
    }

    public int getValue(){
      return value;
    }

    public StrandedFeature.Strand getStrand(){
     return strand;
    }
  }
}


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 


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