org.biojava.nbio.alignment.SimpleGapPenalty Maven / Gradle / Ivy
/*
* 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/
*
* Created on June 9, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment;
import java.io.Serializable;
import org.biojava.nbio.alignment.template.GapPenalty;
/**
* Implements a data structure for the gap penalties used during a sequence alignment routine.
*
* @author Mark Chapman
*/
public class SimpleGapPenalty implements GapPenalty, Serializable {
private static final long serialVersionUID = 3945671344135815456L;
private static int dgop = 10, dgep = 1;
/**
* Sets the default gap extension penalty.
*
* @param gep the default gap extension penalty
*/
public static void setDefaultExtensionPenalty(int gep) {
dgep = gep;
}
/**
* Sets the default gap open penalty.
*
* @param gop the default gap open penalty
*/
public static void setDefaultOpenPenalty(int gop) {
dgop = gop;
}
private GapPenalty.Type type;
private int gop, gep;
/**
* Creates a new set of gap penalties using the defaults.
*/
public SimpleGapPenalty() {
this(dgop, dgep);
}
/**
* Creates a new set of gap penalties.
*
* @param gop the gap open penalty; should be nonnegative
* @param gep the gap extension penalty; should be nonnegative
*/
public SimpleGapPenalty(int gop, int gep) {
this.gop = -Math.abs(gop);
this.gep = -Math.abs(gep);
setType();
}
/**
* Returns the negative of the extension penalty passed to the constructor.
*/
@Override
public int getExtensionPenalty() {
return gep;
}
/**
* Returns the negative of the opening penalty passed to the constructor.
*/
@Override
public int getOpenPenalty() {
return gop;
}
@Override
public Type getType() {
return type;
}
/**
* @param gep Should be nonnegative
*/
@Override
public void setExtensionPenalty(int gep) {
this.gep = -Math.abs(gep);
setType();
}
/**
* @param gop Should be nonnegative
*/
@Override
public void setOpenPenalty(int gop) {
this.gop = -Math.abs(gop);
setType();
}
// helper method to set the type given the open and extension penalties
private void setType() {
type = (gop == 0) ? GapPenalty.Type.LINEAR : ((gep == 0) ? GapPenalty.Type.CONSTANT : GapPenalty.Type.AFFINE);
}
}