Package pal.datatype

Class 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

      Fields 
      Modifier and Type Field Description
      static java.lang.String[] all  
      double[][] IUPACPenalties  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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()