big bug on grouping factories fixed

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@294 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java

@@ -15,16 +15,12 @@ public class HashPeptideSet extends HashKey4GroupsSet {
 	 */
 	private static final Logger logger = Logger.getLogger(HashPeptideSet.class);
 
-	private HashMap<Integer, HashPeptide> getHashPeptide = new HashMap<Integer, HashPeptide>(
-			0);
-
 	public HashPeptideSet() {
 		// logger.debug("HashPeptideSet begin");
 	}
 
 	@Override
 	public void clear() {
-		getHashPeptide = new HashMap<Integer, HashPeptide>(0);
 		super.clear();
 	}
 
@@ -36,10 +32,20 @@ public class HashPeptideSet extends HashKey4GroupsSet {
 		HashPeptide temp = new HashPeptide(sampleScan, sequence);
 
 		if (this.add(temp)) {
-			getHashPeptide.put(temp.hashCode(), temp);
+			//this HashPeptide is new
 			return (temp);
 		}
-		return getHashPeptide.get(temp.hashCode());
+		else {
+			// find the existing instance of the same peptide scan :
+			for (HashKey4Groups toCompare:this) {
+				HashPeptide hashPeptideToCompare = (HashPeptide) toCompare;
+				if (temp.equals(hashPeptideToCompare)) {
+					return hashPeptideToCompare;
+				}
+			}
+		}
+		logger.error("ERROR this might not appear");
+		return temp;
 	}
 
 }

xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java

 package fr.inra.pappso.xtandempipeline.grouping;
 
-import java.util.HashMap;
-
 import org.apache.log4j.Logger;
 
 public class HashProteinSet extends HashKey4GroupsSet {
@@ -16,9 +14,6 @@ public class HashProteinSet extends HashKey4GroupsSet {
 	 */
 	private static final Logger logger = Logger.getLogger(HashProteinSet.class);
 
-	private HashMap<Integer, HashProtein> getHashProtein = new HashMap<Integer, HashProtein>(
-			0);
-
 	public HashProteinSet() {
 		// logger.debug("HashPeptideSet begin");
 	}
@@ -27,15 +22,24 @@ public class HashProteinSet extends HashKey4GroupsSet {
 		HashProtein temp = new HashProtein(accession);
 
 		if (this.add(temp)) {
-			getHashProtein.put(temp.hashCode(), temp);
+			//this HashProtein is new
 			return (temp);
 		}
-		return getHashProtein.get(temp.hashCode());
+		else {
+			// find the existing instance of the same sample scan :
+			for (HashKey4Groups toCompare:this) {
+				HashProtein hashProtToCompare = (HashProtein) toCompare;
+				if (temp.equals(hashProtToCompare)) {
+					return hashProtToCompare;
+				}
+			}
+		}
+		logger.error("ERROR this might not appear");
+		return temp;
 	}
 
 	@Override
 	public void clear() {
-		getHashProtein = new HashMap<Integer, HashProtein>(0);
 		super.clear();
 	}
 

xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java

@@ -2,7 +2,6 @@ package fr.inra.pappso.xtandempipeline.grouping;
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.HashSet;
 
 import org.apache.log4j.Logger;
@@ -18,9 +17,6 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 	private static final Logger logger = Logger
 			.getLogger(HashSampleScanSet.class);
 
-	private HashMap<Integer, HashSampleScan> getSampleScan = new HashMap<Integer, HashSampleScan>(
-			0);
-
 	public HashSampleScanSet() {
 	}
 
@@ -35,10 +31,19 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 		HashSampleScan temp = new HashSampleScan(scan, msRun);
 
 		if (this.add(temp)) {
-			getSampleScan.put(temp.hashCode(), temp);
+			//this hashSampleScan is new
 			return (temp);
 		}
-		return getSampleScan.get(temp.hashCode());
+		else {
+			// find the existing instance of the same sample scan :
+			for (HashSampleScan toCompare:this) {
+				if (temp.equals(toCompare)) {
+					return toCompare;
+				}
+			}
+		}
+		logger.error("ERROR this might not appear");
+		return temp;
 	}
 
 	public void loggerDebug() {
@@ -65,22 +70,7 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 
 	@Override
 	public void clear() {
-		getSampleScan = new HashMap<Integer, HashSampleScan>(0);
 		super.clear();
 	}
 
-	// private String getFingerPrint() {
-	// ArrayList<String> strList = new ArrayList<String>(this.size());
-	// for (HashSampleScan sampleScan:this) {
-	// strList.add(sampleScan.getFingerPrint());
-	// }
-	// Collections.sort(strList);
-	// String code = new String();
-	// for (String sampleScanStr:strList) {
-	// code.concat(sampleScanStr);
-	// }
-	//
-	// return code;
-	// }
-
 }