jaligner.matrix
Class Matrix

java.lang.Object
  jaligner.matrix.Matrix

All Implemented Interfaces:

java.io.Serializable

public class Matrix

extends java.lang.Object

implements java.io.Serializable

Scoring matrix.

Author:

Ahmed Moustafa (ahmed@users.sf.net)

See Also:

Serialized Form

Field Summary

static int

SIZE The size of the scoring matrix.

Constructor Summary

Matrix(java.lang.String id, float[][] scores)

Method Summary

java.lang.String	getId()
float	getScore(char a, char b)
float[][]	getScores()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SIZE

public static final int SIZE

The size of the scoring matrix. It is the number of the characters in the ASCII table. It is more than the 20 amino acids just to save the processing time of the mapping.

See Also:

Constant Field Values

Constructor Detail

Matrix

public Matrix(java.lang.String id,
              float[][] scores)

Method Detail

getId

public java.lang.String getId()

Returns:

Returns the id.

getScores

public float[][] getScores()

Returns:

Returns the scores.

getScore

public float getScore(char a,
                      char b)

Parameters:

a -

b -

Returns:

score