git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@346 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MapDb/PeptideStore.java

@@ -11,9 +11,10 @@ public class PeptideStore {
 	MsRunSet msRunSet = new MsRunSet();
 
 	static public PeptideStore getInstance() {
-		logger.debug("getInstance");
+		//logger.debug("getInstance");
 		if (store == null) {
 			store = new PeptideStoreClassic();
+			//store = new PeptideStoreMapDb();
 		}
 		return (store);
 	}

xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRunSet.java

@@ -10,63 +10,68 @@ import org.apache.log4j.Logger;
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataSource;
 
-public class MsRunSet extends HashSet<MsRun>{
+public class MsRunSet extends HashSet<MsRun> {
 	/**
 	 * 
 	 */
 	private static final long serialVersionUID = 1859166854395591445L;
-	
+
 	private static final Logger logger = Logger.getLogger(MsRunSet.class);
-	
-	private HashMap<String,MsRun> name2msRun= new HashMap<String,MsRun>(0);
+
+	private HashMap<String, MsRun> name2msRun = new HashMap<String, MsRun>(0);
 
 	public MsRunSet() {
 	}
 
 	/**
-	 * @param Take name of sample, this is normally the filename without extension
+	 * @param Take
+	 *            name of sample, this is normally the filename without
+	 *            extension
 	 * @return MsRun instance
 	 */
 	public MsRun getInstance(String sampleName) {
-		//Remove file extension for storing sample
+		// Remove file extension for storing sample
 		sampleName = sampleName.replaceAll("\\.xml$", "");
 		sampleName = sampleName.replaceAll("\\.dat$", "");
-	
+
 		if (name2msRun.containsKey(sampleName)) {
+			// logger.debug("get MsRun by sample name " + sampleName);
 			return name2msRun.get(sampleName);
 		}
-		logger.debug("add "+sampleName);
+		// logger.debug("add new MsRun with sample name " + sampleName);
 		MsRun msRun = new MsRun(sampleName);
 		name2msRun.put(sampleName, msRun);
 		this.add(msRun);
 		return msRun;
 	}
-	
+
 	/**
-	 * @param Take name of sample from file by removing extension.
+	 * @param Take
+	 *            name of sample from file by removing extension.
 	 * @return MsRun instance
-	 * @throws MSMSException 
+	 * @throws MSMSException
 	 */
-	public MsRun getInstance(IdentificationDataSource sampleFile) throws MSMSException {
+	public MsRun getInstance(IdentificationDataSource sampleFile)
+			throws MSMSException {
 		String sampleName = sampleFile.getName();
-		
-		//Remove file extension for storing sample
-		sampleName = sampleName.replaceAll("\\.xml$", "");
-		sampleName = sampleName.replaceAll("\\.dat$", "");
-		
-		if (name2msRun.containsKey(sampleName)) {
-			return name2msRun.get(sampleName);
-		}
-		logger.debug("add "+sampleName);
-		MsRun msRun = new MsRun(sampleName);
-		name2msRun.put(sampleName, msRun);
-		this.add(msRun);
-		return msRun;
+
+		return getInstance(sampleName);
 	}
-	
-	public ArrayList<MsRun> getMsRunList(){
+
+	public ArrayList<MsRun> getMsRunList() {
 		ArrayList<MsRun> msRunList = new ArrayList<MsRun>(this);
 		Collections.sort(msRunList);
 		return (msRunList);
 	}
+
+	public boolean containsMsRunFromThisDataSource(
+			IdentificationDataSource dataSourceToParse) throws MSMSException {
+		String sampleName = dataSourceToParse.getName();
+		sampleName = sampleName.replaceAll("\\.xml$", "");
+		sampleName = sampleName.replaceAll("\\.dat$", "");
+		if (name2msRun.containsKey(sampleName)) {
+			return true;
+		}
+		return false;
+	}
 }

xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java

@@ -37,23 +37,24 @@ public class individual extends process {
 
 		// Ecrire le process et penser à relever des StopException
 		for (int i = 0; i < dataSources.size(); i++) {
+			IdentificationDataSource dataSourceToParse = dataSources.get(i);
 			// parsing
 			this.set_view("Analysing file : " + (i + 1) + "/"
 					+ dataSources.size() + "\n" + "Parsing file : "
-					+ dataSources.get(i).getName());
+					+ dataSourceToParse.getName());
 
 			// Is sample exist? Get previous identification
 			Identification identtemp = null;
 			for (int m = 0; m < identifications.size(); m++) {
-				MsRunSet samples = identifications.get(m).get_samples();
-				MsRun test = samples.getInstance(dataSources.get(i));
-				if (test == null) {
-					String message = "MsRun test is null";
-					logger.error(message);
-					throw new MSMSException(message);
+				logger.debug("identifications.size() "+identifications.size());
+				MsRunSet samples = identifications.get(m).getMsRunSet();
+				for (MsRun sample : samples) {
+					logger.debug("msRun name : " + sample.getSampleName());
 				}
-				if (samples.contains(test))
+				if (samples.containsMsRunFromThisDataSource(dataSourceToParse)) {
 					identtemp = identifications.get(m);
+					logger.debug("found " + dataSourceToParse.getName());
+				}
 			}
 			// xtandem handler;
 			// if (identtemp != null)
@@ -66,8 +67,7 @@ public class individual extends process {
 			// identifications.add(handler.get_identifications());
 
 			// Load identification from datasource
-			identifications.add(dataSources.get(i)
-					.loadIdentification(identtemp));
+			identifications.add(dataSourceToParse.loadIdentification(identtemp));
 
 			// verification pas arreté
 			if (this.isStop())