jaligner.matrix
Class MatrixLoader

java.lang.Object
  jaligner.matrix.MatrixLoader

public class MatrixLoader

extends java.lang.Object

Scoring matrices loader from a jar file or a file system.

Author:

Ahmed Moustafa (ahmed@users.sf.net)

Constructor Summary

MatrixLoader()

Method Summary

static java.util.Collection	list() Returns a list of the scoring matrices in the matrices home directory
static java.util.Collection	list(boolean sort) Returns a list of the scoring matrices in the matrices home directory
static Matrix	load(NamedInputStream nis) Loads scoring matrix from InputStream
static Matrix	load(java.lang.String matrix) Loads scoring matrix from Jar file or file system.

Methods inherited from class java.lang.Object

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

Constructor Detail

MatrixLoader

public MatrixLoader()

Method Detail

load

public static Matrix load(java.lang.String matrix)
                   throws MatrixLoaderException

Loads scoring matrix from Jar file or file system.

Parameters:

matrix - to load

Returns:

loaded matrix

Throws:

MatrixLoaderException

See Also:

Matrix

load

public static Matrix load(NamedInputStream nis)
                   throws MatrixLoaderException

Loads scoring matrix from InputStream

Parameters:

nis - named input stream

Returns:

loaded matrix

Throws:

MatrixLoaderException

See Also:

Matrix, NamedInputStream

list

public static java.util.Collection list(boolean sort)
                                 throws MatrixLoaderException

Returns a list of the scoring matrices in the matrices home directory

Parameters:

sort - flag to sort the list or not

Returns:

sorted array of scoring matrices

Throws:

MatrixLoaderException

list

public static java.util.Collection list()
                                 throws MatrixLoaderException

Returns a list of the scoring matrices in the matrices home directory

Returns:

sorted array of scoring matrices

Throws:

MatrixLoaderException