/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$
*/
package org.eurocarbdb.applications.ms.glycopeakfinder.io;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import org.eurocarbdb.applications.ms.glycopeakfinder.io.PeakListLoader;
import org.eurocarbdb.applications.ms.glycopeakfinder.io.PeakListLoaderExeption;
import org.eurocarbdb.applications.ms.glycopeakfinder.storage.GPPeak;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
public class PeakListLoaderFlexAnalysis implements PeakListLoader
{
ArrayList<GPPeak> m_aPeaks = new ArrayList<GPPeak>();
public ArrayList<GPPeak> loadPeaklist(File a_hFile) throws PeakListLoaderExeption
{
boolean t_bMass;
boolean t_bIntsensity;
this.m_aPeaks.clear();
Document t_objDocument;
try
{
t_objDocument = new SAXBuilder().build(a_hFile);
Element t_objRoot = t_objDocument.getRootElement();
for (Iterator t_iterPK = t_objRoot.getChildren().iterator(); t_iterPK.hasNext();)
{
Element t_objSubElement = (Element) t_iterPK.next();
GPPeak t_objPeak = new GPPeak();
t_bMass = false;
t_bIntsensity = false;
for (Iterator t_iterSubs = t_objSubElement.getChildren().iterator(); t_iterSubs.hasNext();)
{
Element t_objElement = (Element) t_iterSubs.next();
if ( t_objElement.getName().equals("area") )
{
t_objPeak.setIntensity( Double.parseDouble(t_objElement.getText()) );
t_bIntsensity = true;
}
else if ( t_objElement.getName().equals("mass") )
{
t_objPeak.setMZ( Double.parseDouble(t_objElement.getText()) );
t_bMass = true;
}
}
if ( !(t_bMass && t_bIntsensity) )
{
throw new PeakListLoaderExeption("Mass or Intensity value missing in file.");
}
this.m_aPeaks.add(t_objPeak);
}
}
catch (JDOMException e)
{
throw new PeakListLoaderExeption(e.getMessage());
}
catch (IOException e)
{
throw new PeakListLoaderExeption(e.getMessage());
}
return this.m_aPeaks;
}
}