Package pal.datatype
Class IUPACPenaltyTable
- java.lang.Object
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- pal.datatype.IUPACPenaltyTable
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- 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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
all
double[][]
IUPACPenalties
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Constructor Summary
Constructors Constructor Description IUPACPenaltyTable()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DataType
getDataType()
double
penalty(int a, int b)
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Method Detail
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penalty
public final double penalty(int a, int b)
- Specified by:
penalty
in interfaceTransitionPenaltyTable
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getDataType
public final DataType getDataType()
- Specified by:
getDataType
in interfaceTransitionPenaltyTable
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