uk.ac.ebi.adfconverter.common.tools.file.reader
Class MAGEReader

java.lang.Object
  uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader

public class MAGEReader

extends java.lang.Object

Class for MAGE-ML file reading Based on the MAGEReader From MAGEstk by Kjell Petersen

Version:

1 ADF MAGE-TOOL - MicroArray Informatics Team / European Bioinformatics Institute (EBI) ArrayExpress License: ============================================================================== Copyright (c) 2002 The European Bioinformatics Institute. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name ArrayExpress must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact arrayexpress@ebi.ac.uk 4. Products derived from this software may not be called "ArrayExpress" nor may "ArrayExpress" appear in their names without prior written permission of the ArrayExpress developers. 5. Redistributions of any form whatsoever must retain the following acknowledgment: "This product includes software developed by ArrayExpress (http://www.ebi.ac.uk/arrayexpress)" THIS SOFTWARE IS PROVIDED BY THE ARRAYEXPRESS GROUP ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ARRAYEXPRESS GROUP OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The European Bioinformatics Institute may publish revised and/or new versions of this license with new releases of ArrayExpress software. ==============================================================================

Author:

Pierre MARGUERITE

Constructor Summary

MAGEReader()
Creates a new instance of MAGEReader

MAGEReader(java.io.File _DTDFile)
Creates a new instance of MAGEReader

Method Summary

MAGEJava	getMAGEobj() Retrieves the MAGE object obtained from MAGE-ML file
MAGEJava	readFile(java.io.File magefile) Reads a MAGE-ML File (converts it in MAGE Object)

Methods inherited from class java.lang.Object

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

Constructor Detail

MAGEReader

public MAGEReader()

Creates a new instance of MAGEReader

MAGEReader

public MAGEReader(java.io.File _DTDFile)

Creates a new instance of MAGEReader

Parameters:

_DTDFile - the MAGE-ML dtd file

Method Detail

getMAGEobj

public MAGEJava getMAGEobj()

Retrieves the MAGE object obtained from MAGE-ML file

Returns:

the MAGEJava object (root object) from the MAGE-ML file

readFile

public MAGEJava readFile(java.io.File magefile)

Reads a MAGE-ML File (converts it in MAGE Object)

Parameters:

magefile - the file to read

Returns:

the MAGEJava object corresponding to the MAGE-ML file. null, if error during reading