/*
* 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 7, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
/**
* Defines a data structure for the gap penalties used during a sequence alignment routine.
*
* @author Mark Chapman
*/
public interface GapPenalty {
/**
* Defines the possible types of gap penalties. This is:
* <ul>
* <li>CONSTANT, if static and the extension penalty is 0
* <li>LINEAR, if static and the open penalty is 0
* <li>AFFINE, if static but neither CONSTANT nor LINEAR
* <li>DYNAMIC, if penalty values change during alignment
* </ul>
*/
enum Type {CONSTANT, LINEAR, AFFINE, DYNAMIC};
/**
* Returns penalty given when an already open gap elongates by a single element
*
* @return gap extension penalty
*/
int getExtensionPenalty();
/**
* Returns penalty given when a deletion or insertion gap first opens
*
* @return gap open penalty
*/
int getOpenPenalty();
/**
* Returns {@link GapPenalty.Type} stored.
*
* @return gap penalty type
*/
Type getType();
/**
* Sets penalty given when an already open gap elongates by a single element
*
* @param gep gap extension penalty
*/
void setExtensionPenalty(int gep);
/**
* Sets penalty given when a deletion or insertion gap first opens
*
* @param gop gap open penalty
*/
void setOpenPenalty(int gop);
}