IUPACPenaltyTable

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Summary:
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Field |
Constr |
Method

Detail:
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Constr |
Method

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.

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
- Constructor Summary
  
  Constructors
  Constructor Description
  
  IUPACPenaltyTable()
- 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()
```

Method Detail
- 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

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