Package pal.datatype

Class IUPACPenaltyTable

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

public class IUPACPenaltyTable extends 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 Details

    • IUPACPenalties

      public double[][] IUPACPenalties
    • all

      public static final String[] all
  • Constructor Details

    • IUPACPenaltyTable

      public IUPACPenaltyTable()
  • Method Details