//=====================================================================
// File: PartialSigNorm.java
// Class: PartialSigNorm
// Package: AFLPcore
//
// Author: James J. Benham
// Date: January 6, 1999
// Contact: james_benham@hmc.edu
//
// Genographer v1.0 - Computer assisted scoring of gels.
// Copyright (C) 1998 Montana State University
//
// 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; version 2
// of the License.
//
// 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.
//
// The GNU General Public License is distributed in the file GPL
//=====================================================================
package AFLPcore;
/**
* This class normalizes a gel. The total signal in a lane is defined
* as the sum of all of the points in a trace. Since the trace is
* simply a set of discrete points that form a curve, the total signal
* may also be thought of as the area under the trace curve, or as
* the integral over the entire size range. The lanes are normalized
* so that the total signal's are equal to the average signal in the
* gel.
*
* This class extends a gel operation. The signal in each lane is
* handled by the Lane
class. There are no options to set.
*
* @author James J. Benham
* @version 1.0.0
* @date January 6, 1999
*/
public class PartialSigNorm extends GelOperation
{
public static double DEFAULT_PERCENT = 0.1;
/**
* Creates a new PartialSigNorm object.
*/
public PartialSigNorm()
{
name = "Normalize on Partial Signal";
descript = "Normalizes the lanes based on the stronger part of the " +
"signal intensity of the lane.";
helpFile = "PartialSigNorm.html";
}
/**
* This normalizes all of the lanes in the Gel based on the signal
* stength of each lane.
*
* @param gel the gel to normalize.
*/
public void doGelOp(Gel gel)
{
double percentage;
double sum;
double minValue;
Lane ln;
double rawTrace[];
// Read in the percentage from the file
String percentStr = ProgOptions.retrieve("BASE_MIN");
if(percentStr == null)
{
percentage = DEFAULT_PERCENT;
System.err.println("BASE_MIN not set in config file." +
"Using default.");
}
else
{
try{
percentage = (new Double(percentStr)).doubleValue();
} catch (NumberFormatException e) {
percentage = DEFAULT_PERCENT;
System.err.println("Bad value for BASE_MIN in " +
"configuration file. Using " +
"default." + e.getMessage());
}
}
DataList lanes = gel.getLanes();
double sigSums[] = new double[lanes.size()];
for(int i=0; i < sigSums.length; i++)
{
ln = (Lane) lanes.dataAt(i);
minValue = percentage*ln.getMaxHeight(ln.getMinSize(),
ln.getMaxSize());
sum = 0;
ln.useTrace(Lane.ORIGINAL);
rawTrace = ln.getTrace();
for(int j=0; j < rawTrace.length; j++)
if(rawTrace[j] > minValue)
sum += rawTrace[j];
sigSums[i] = sum;
}
double normValue;
// use the average signal strength as the value to normalize to
sum = 0;
for(int i=0; i < sigSums.length; i++)
sum += sigSums[i];
normValue = sum / lanes.size();
double convertFactor;
double normTrace[];
for(int i=0; i < lanes.size(); i++)
{
ln = (Lane) lanes.dataAt(i);
// make sure we have the raw trace
// We already selected it above
rawTrace = ln.getTrace();
// create the normalized trace
normTrace = new double[rawTrace.length];
convertFactor = normValue/sigSums[i];
for(int j=0; j < rawTrace.length; j++)
normTrace[j] = rawTrace[j] * convertFactor;
// set the normalized trace and us it
ln.setNormTrace(normTrace);
ln.useTrace(Lane.NORMALIZED);
}
}
/**
* No options for this operation, so null
is returned.
*
* @return null
*/
public Option[] getOptions()
{
return null;
}
/**
* Since there are no options for this operation, this method will
* do absolutely nothing.
*/
public void setOptions(Option[] opts)
{
// nothing to set.
}
/**
* Gives the name of this gel operation
*
* @return the name
*/
public String getName()
{
return name;
}
/**
* Gives a one sentence description of this gel operation.
*
* @return the description
*/
public String getDescription()
{
return descript;
}
/**
* Gives a file that is the help file for this gel operation
*
* @return a plaintext of html file containing help information
*/
public String getHelpFile()
{
return helpFile;
}
}