pal.datatype
Class IUPACPenaltyTable

java.lang.Object
  extended by pal.datatype.IUPACPenaltyTable
All Implemented Interfaces:
TransitionPenaltyTable

public class IUPACPenaltyTable
extends java.lang.Object
implements TransitionPenaltyTable

Implements a table of transition penalties for a DNA states and IUPAC ambiguous states. A mismatch is normalized to a penalty of 1.0
Used for alignment scoring.

Version:
$Id: IUPACPenaltyTable.java,v 1.3 2001/07/13 14:39:13 korbinian Exp $
Author:
Alexei Drummond

Field Summary
static java.lang.String[] all
           
 double[][] IUPACPenalties
           
 
Constructor Summary
IUPACPenaltyTable()
           
 
Method Summary
 DataType getDataType()
           
 double penalty(int a, int b)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

IUPACPenalties

public double[][] IUPACPenalties

all

public static final java.lang.String[] all
Constructor Detail

IUPACPenaltyTable

public IUPACPenaltyTable()
Method Detail

penalty

public final double penalty(int a,
                            int b)
Specified by:
penalty in interface TransitionPenaltyTable

getDataType

public final DataType getDataType()
Specified by:
getDataType in interface TransitionPenaltyTable