pal.datatype
Class IUPACPenaltyTable
java.lang.Object
|
+--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.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
IUPACPenalties
public double[][] IUPACPenalties
all
public static final java.lang.String[] all
IUPACPenaltyTable
public IUPACPenaltyTable()
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