jaligner.matrix.Matrix Class Reference

Inheritance diagram for jaligner.matrix.Matrix:

Collaboration diagram for jaligner.matrix.Matrix:

Public Member Functions
	Matrix (String id, float[][] scores)
String	getId ()
float[][]	getScores ()
float	getScore (char a, char b)

Static Public Attributes
static final int	SIZE = 127

Detailed Description

Scoring matrix.

Author

Ahmed Moustafa (ahmed.nosp@m.@use.nosp@m.rs.sf.nosp@m..net)

Constructor & Destructor Documentation

jaligner.matrix.Matrix.Matrix	(	String	id,
		float	scores[][]
	)

Member Function Documentation

String jaligner.matrix.Matrix.getId

(

)

Returns

Returns the id.

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float jaligner.matrix.Matrix.getScore	(	char	a,
		char	b
	)

Parameters

a
b

Returns

score

float [][] jaligner.matrix.Matrix.getScores

(

)

Returns

Returns the scores.

Member Data Documentation

final int jaligner.matrix.Matrix.SIZE = 127

static

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.

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The documentation for this class was generated from the following file:

• java/jaligner/matrix/Matrix.java