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Commit c66ca1b1 authored by Ludovic Cottret's avatar Ludovic Cottret
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remove unused class

parent 0494a65a
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met4j-graph/src/main/java/fr/inra/toulouse/metexplore/met4j_graph/computation/analysis/SbmlScopeCompounds.java deleted 100755 → 0
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/*******************************************************************************
* Copyright INRA
*
* Contact: ludovic.cottret@toulouse.inra.fr
*
*
* This software is governed by the CeCILL license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.
******************************************************************************/
package fr.inra.toulouse.metexplore.met4j_graph.computation.analysis;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.HashSet;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.text.parser.ParseException;
import fr.inra.toulouse.metexplore.met4j_graph.core.ScopeCompounds;
import fr.inra.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import fr.inra.toulouse.metexplore.met4j_core.io.JSBMLToBionetwork;
// TODO: Auto-generated Javadoc
/**
* The Class SbmlScopeCompounds.
*/
public class SbmlScopeCompounds {
/**
* The main method.
*
* @param args the arguments
*/
public static void main(String[] args) {
Set<String> listOfInCpds = new HashSet<String>();
Set<String> listOfBootstrapCpds = new HashSet<String>();
String sbmlFile = args[0];
String listOfCompoundsFile = args[1];
String fileOut = args[2];
String flagOnlyResults = args[3];
String encodeStr = args[4];
String flagRevReactions = args[5];
Boolean useReversibleReactionsOnlyOnce = false;
if(flagRevReactions.equalsIgnoreCase("T")) {
useReversibleReactionsOnlyOnce = true;
}
Boolean encode = false;
if(encodeStr.compareTo("T") == 0) {
encode = true;
}
Boolean onlyResults = false;
if(flagOnlyResults.compareTo("T") == 0) {
onlyResults = true;
}
FileInputStream in;
try {
in = new FileInputStream(listOfCompoundsFile);
InputStreamReader ipsr=new InputStreamReader(in);
BufferedReader br=new BufferedReader(ipsr);
String ligne;
while ((ligne=br.readLine())!=null){
String[] tab = ligne.split("\\t");
String id;
id = tab[0];
String type = tab[1];
if(type.compareTo("I") == 0)
listOfInCpds.add(id);
else if (type.compareTo("B") == 0) {
listOfBootstrapCpds.add(id);
}
}
} catch (FileNotFoundException e1) {
e1.printStackTrace();
} catch (IOException e1) {
e1.printStackTrace();
}
JSBMLToBionetwork reader = new JSBMLToBionetwork(sbmlFile);
BioNetwork bn = reader.getBioNetwork();
// Here, we do not filter the reactionNodes
ScopeCompounds scope = new ScopeCompounds(bn, listOfInCpds, listOfBootstrapCpds, "", new HashSet<String>(), useReversibleReactionsOnlyOnce, true);
System.err.println("Number of reactions : "+bn.getBiochemicalReactionList().size());
System.err.println("Number of compounds : "+bn.getPhysicalEntityList().size());
while(scope.run() != 0) { // While new compounds are added
;
}
scope.createScopeNetwork();
System.err.println("Fileout : "+fileOut);
String fileAttributs = fileOut+".attributes";
String fileReactions = fileOut+".reactions";
String fileCpds = fileOut+".cpds";
String fileSbml = fileOut+".xml";
String fileInvSbml = fileOut+"_inv.xml";
try {
scope.writeAttributeFile(fileAttributs, encode, onlyResults);
scope.writeListOfReactions(fileReactions, encode);
scope.writeListOfCompounds(fileCpds, encode);
scope.writeClustersFiles(fileOut, encode);
try {
scope.writeScopeAsSbml(fileSbml);
scope.writeInvScopeAsSbml(fileInvSbml);
} catch (SBMLException | XMLStreamException | ParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
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