JAligner

jaligner.matrix
Class MatrixLoader

java.lang.Object
  extended byjaligner.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

JAligner

Ahmed Moustafa (ahmed@users.sf.net)SourceForge.net
The source code of JAligner is licensed under The GNU General Public License (GPL)