GCFrameAlgorithm.java

/* GCFrameAlgorithm.java
 *
 * created: Tue Dec 15 1998
 *
 * This file is part of Artemis
 * 
 * Copyright (C) 1998,1999,2000  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/plot/GCFrameAlgorithm.java,v 1.1 2004-06-09 09:51:28 tjc Exp $
 */

package uk.ac.sanger.artemis.plot;

import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.Range;

/**
 *  Objects of this class have one useful method - getValues (), which takes a
 *  range of bases and returns three floating point numbers, which are the
 *  percent GC content in each frame.  The Strand to use is set in the
 *  constructor.
 *
 *  @author Kim Rutherford
 *  @version $Id: GCFrameAlgorithm.java,v 1.1 2004-06-09 09:51:28 tjc Exp $
 **/

public class GCFrameAlgorithm extends BaseAlgorithm {
  /**
   *  Create a new GCFrameAlgorithm object.
   *  @param strand The Strand to do the calculation on.
   **/
  public GCFrameAlgorithm (final Strand strand) {
    super (strand, makeName (strand), "gc_frame");

    setScalingFlag (true);
  }

  /**
   *  This is used as temporary storage by getValues ().
   **/
  private int gc_counts [] = new int [getValueCount ()];

  /**
   *  Return the percent gc between a pair of bases in each of the three
   *  frames.
   *  @param start The start base (included in the range).
   *  @param end The end base (included in the range).  If the start/end pair
   *    doesn't give a multiple of three bases end is moved down so that it is
   *    a multiple of three.
   *  @param values The three results are returned in this array, hence it
   *    should be three long.  The first value is the gc content of positions
   *    start, start+3, start+6, etc, the second value is start+1, start+4,
   *    etc.
   **/
  public void getValues (int start, int end, final float [] values) {
    if (isRevCompDisplay ()) {
      final int new_end =
        getStrand ().getBases ().getComplementPosition (start);
      final int new_start =
        getStrand ().getBases ().getComplementPosition (end);

      end = new_end;
      start = new_start;
    }

    // add 1 or 2 if necessary to make the range a multiple of 3
    if (getStrand ().isForwardStrand ()) {
      end -= (end - start + 1) % 3;
    } else {
      start += (end - start + 1) % 3;
    }

    for (int i = 0 ; i < getValueCount () ; ++i) {
      gc_counts[i] = 0;
    }
    
    final String sub_sequence;

    try {
      sub_sequence = getStrand ().getRawSubSequence (new Range (start, end));
    } catch (OutOfRangeException e) {
      throw new Error ("internal error - unexpected exception: " + e);
    }

    final int sub_sequence_length = sub_sequence.length ();

    if (getStrand ().isForwardStrand ()) {
      for (int i = 0 ; i < sub_sequence_length ; i += 3) {
        for (int frame = 0 ; frame < 3 ; ++frame) {
          final char this_char = sub_sequence.charAt (i + frame);

          if (this_char == 'g' || this_char == 'c') {
            ++gc_counts[(frame + start) % 3];
          }
        }
      }
    } else {
      final int whole_sequence_length = getStrand ().getSequenceLength ();

      final int whole_sequence_length_mod3 = whole_sequence_length % 3;

      for (int i = 0 ;
           i < sub_sequence_length ;
           i += 3) {
        for (int frame = 0 ; frame < 3 ; ++frame) {
          final char this_char = sub_sequence.charAt (i + frame);

          if (this_char == 'g' || this_char == 'c') {
            ++gc_counts[(frame + start + 3 - whole_sequence_length_mod3) % 3];
          }
        }
      }
    }

    for (int frame = 0 ; frame < 3 ; ++frame) {
      // multiply by 3 because we are taking every third base
      values[frame] = 1.0F * gc_counts[frame]/sub_sequence_length * 3 * 100;
    }
  }

  /**
   *  Return the number of values a call to getValues () will return - three
   *  in this case.
   **/
  public int getValueCount () {
    return 3;
  }

  /**
   *  Return the default or optimal window size.
   *  @return null is returned if this algorithm doesn't have optimal window
   *    size.
   **/
  public Integer getDefaultWindowSize () {
    final Integer super_window_size = super.getDefaultWindowSize ();
    if (super_window_size != null) {
      // the superclass version of getDefaultWindowSize () returns non-null
      // iff the user has set the window size in the options file
      return super_window_size;
    }
    return new Integer (120);
  }

  /**
   *  Return the default maximum window size for this algorithm.
   *  @return null is returned if this algorithm doesn't have maximum window
   *    size.
   **/
  public Integer getDefaultMaxWindowSize () {
    final Integer super_max_window_size = super.getDefaultMaxWindowSize ();
    if (super_max_window_size != null) {
      // the superclass version of getDefaultMaxWindowSize () returns non-null
      // iff the user has set the max window size in the options file
      return super_max_window_size;
    }
    return new Integer (500);
  }

  /**
   *  Return the default minimum window size for this algorithm.
   *  @return null is returned if this algorithm doesn't have minimum window
   *    size.
   **/
  public Integer getDefaultMinWindowSize () {
    final Integer super_min_window_size = super.getDefaultMinWindowSize ();
    if (super_min_window_size != null) {
      // the superclass version of getDefaultMinWindowSize () returns non-null
      // iff the user has set the minimum window size in the options file
      return super_min_window_size;
    }
    return new Integer (24);
  }

  /**
   *  Return the default or optimal step size.
   *  @return null is returned if this algorithm doesn't have optimal step
   *    size.
   **/
  public Integer getDefaultStepSize (int window_size) {
    if (window_size > 8) {
      return new Integer (window_size / 8);
    } else {
      return null;
    }
  }

  /**
   *  Return the maximum value of this algorithm.
   *  @return The maximum is 100.
   **/
  protected Float getMaximumInternal () {
    return new Float (100);
  }

  /**
   *  Return the minimum value of this algorithm.
   *  @return The minimum is 0.
   **/
  protected Float getMinimumInternal () {
    return new Float (0);
  }

  /**
   *  Return the average value of function over the whole strand.
   *  @return null is returned if this algorithm doesn't have an average or if
   *    the average can't be calculated.
   **/
  public Float getAverage () {
    return new Float (getStrand ().getBases ().getAverageGCPercent ());
  }

  /**
   *  Returns "GC Frame Plot" if the given strand is a forward strand
   *  otherwise returns "Reverse GC Frame Plot".
   **/
  private static String makeName (final Strand strand) {
    if (strand.isForwardStrand ()) {
      return "GC Frame Plot";
    } else {
      return "Reverse GC Frame Plot";
    }
  }
}