Package pal.datatype
Class IUPACPenaltyTable
java.lang.Object
pal.datatype.IUPACPenaltyTable
- All Implemented Interfaces:
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.
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 Details
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IUPACPenalties
public double[][] IUPACPenalties -
all
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Constructor Details
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IUPACPenaltyTable
public IUPACPenaltyTable()
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Method Details
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penalty
public final double penalty(int a, int b) - Specified by:
penalty
in interfaceTransitionPenaltyTable
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getDataType
- Specified by:
getDataType
in interfaceTransitionPenaltyTable
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