GroupAverager.java :  » Development » TreeView-1.1.4r5 » edu » stanford » genetics » treeview » plugin » karyoview » Java Open Source

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TreeView 1.1.4r5 » edu » stanford » genetics » treeview » plugin » karyoview » GroupAverager.java
/* BEGIN_HEADER                                              Java TreeView
*
* $Author: alokito $
* $RCSfile: GroupAverager.java,v $
* $Revision: 1.2 $
* $Date: 2007/02/03 07:26:48 $
* $Name:  $
*
* This file is part of Java TreeView
* Copyright (C) 2001-2003 Alok Saldanha, All Rights Reserved. Modified by Alex Segal 2004/08/13. Modifications Copyright (C) Lawrence Berkeley Lab.
*
* This software is provided under the GNU GPL Version 2. In particular, 
*
* 1) If you modify a source file, make a comment in it containing your name and the date.
* 2) If you distribute a modified version, you must do it under the GPL 2.
* 3) Developers are encouraged but not required to notify the Java TreeView maintainers at alok@genome.stanford.edu when they make a useful addition. It would be nice if significant contributions could be merged into the main distribution.
*
* A full copy of the license can be found in gpl.txt or online at
* http://www.gnu.org/licenses/gpl.txt
*
* END_HEADER 
*/
package edu.stanford.genetics.treeview.plugin.karyoview;

import edu.stanford.genetics.treeview.*;

/**
* encapsulates routines common to averagers of groups of things
*/
abstract class GroupAverager extends Averager {
  /**
  * the sole method to be implemented by subclasses, which things to average?
  */
  abstract protected ChromosomeLocus [] getContributors(ChromosomeLocus locus);
  abstract protected String getPre();
  public String[] getDescription(ChromosomeLocus locus, int col) {
    HeaderInfo geneInfo = karyoView.getGeneInfo();
    if (locus == null) {
      message[0] = "Locus is null";
      message[1] = "";
    } else {
      ChromosomeLocus []cont = getContributors(locus);
      message[0] = getPre() + " locus " + geneInfo.getHeader(locus.getCdtIndex(), "YORF");
      message[1] = "Mean of " + cont.length + " loci: " + summarizeYorf(cont);
    }
    return message;
  }
  
  private String summarizeYorf(ChromosomeLocus [] loci) {
    HeaderInfo geneInfo = karyoView.getGeneInfo();
    if (loci.length == 0) {
      return "No loci contribute";
    }
    try {
      if (loci.length < 101 ) {
        String ret = geneInfo.getHeader(loci[0].getCdtIndex(), "YORF");
        for(int i = 1; i < loci.length; i++) {
          if (loci[i] != null) {
            ret += ", " + geneInfo.getHeader(loci[i].getCdtIndex(), "YORF");
          }
        }
        return ret;
      } else {
        return "more than 100 loci contribute";
      }
    } catch (Exception e) {
      LogBuffer.println("failed to summarize loci in GroupAverager!: " + e.toString());
      return "failed to summarize loci!: " + e.toString();
    }
  }
  
  public double getValue(ChromosomeLocus locus, int col) {
    if (locus == null) return 0.0;
    int row = locus.getCdtIndex();
    ChromosomeLocus [] loci = getContributors(locus);
    double sum = 0.0;
    int n = 0;
    DataMatrix dataMatrix = karyoView.getDataMatrix();
    int numCol = karyoView.getNumCol();
    for (int i = 0; i < loci.length; i++) {
      if (loci[i] == null) continue;
      int index = loci[i].getCdtIndex();
      if (index == -1) continue;

      sum += dataMatrix.getValue(col,  index);
      n++;
    }
    return sum/n;
  }
  protected boolean isNodata(ChromosomeLocus locus) {
    DataMatrix dataMatrix = karyoView.getDataMatrix();
    int numCol = karyoView.getNumCol();
    try {
      double value = dataMatrix.getValue( karyoView.getCurrentCol() , locus.getCdtIndex());
      return (karyoView.getNodata() == value);
    } catch (java.lang.ArrayIndexOutOfBoundsException e) {
//       LogPanel.println("GroupAverager.isNoData() got cdt index " + locus.getCdtIndex() + " out of bounds ");
      return true;
    }
  }
  protected double getDist(ChromosomeLocus first, ChromosomeLocus second) {
    int firstArm = first.getArm();
    int secondArm = second.getArm();
    if (firstArm == secondArm) {
      return Math.abs(first.getPosition() - second.getPosition());
    } else {
      return Math.abs(first.getPosition() + second.getPosition());
    }
  }
  protected double square(double pos) {
    return pos * pos;
  }
  
}


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