SubstScoreMatrix (JEBL2 lib API)

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java.lang.Object
- jebl.evolution.align.scores.Scores
- - jebl.evolution.align.scores.SubstScoreMatrix

All Implemented Interfaces:

ScoreMatrix
```
public class SubstScoreMatrix
extends Scores
```
Version:

$Id: SubstScoreMatrix.java 360 2006-06-22 07:42:48Z pepster $

Author:

Alexei Drummond

- Field Summary
  - Fields inherited from class jebl.evolution.align.scores.Scores
    score
- Constructor Summary
  
  Constructors
  Constructor Description
  
  SubstScoreMatrix(RateMatrix rateMatrix)
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  java.lang.String getAlphabet()
  
  java.lang.String getName()
  - Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
  - Methods inherited from class jebl.evolution.align.scores.Scores
    duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps, toString

- Constructor Detail
  - SubstScoreMatrix
```
public SubstScoreMatrix(RateMatrix rateMatrix)
```
- Method Detail
  - getName
```
public java.lang.String getName()
```
    Returns:
    
    human readable name
  - getAlphabet
```
public java.lang.String getAlphabet()
```
    Returns:
    
    a string containing the valid characters for this score matrix.

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http://code.google.com/p/jebl2/