performance problem fixed using hashmap

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@295 b8ef2a07-7df7-436f-90b9-41648038564b

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

@@ -15,6 +15,9 @@ public class HashPeptideSet extends HashKey4GroupsSet {
 	 */
 	private static final Logger logger = Logger.getLogger(HashPeptideSet.class);
 
+	private HashMap<HashPeptide, HashPeptide> mapHashPeptide = new HashMap<HashPeptide, HashPeptide>(
+			0);
+
 	public HashPeptideSet() {
 		// logger.debug("HashPeptideSet begin");
 	}
@@ -32,20 +35,13 @@ public class HashPeptideSet extends HashKey4GroupsSet {
 		HashPeptide temp = new HashPeptide(sampleScan, sequence);
 
 		if (this.add(temp)) {
-			//this HashPeptide is new
+			// this HashPeptide is new
+			this.mapHashPeptide.put(temp, temp);
 			return (temp);
-		}
-		else {
+		} else {
 			// find the existing instance of the same peptide scan :
-			for (HashKey4Groups toCompare:this) {
-				HashPeptide hashPeptideToCompare = (HashPeptide) toCompare;
-				if (temp.equals(hashPeptideToCompare)) {
-					return hashPeptideToCompare;
-				}
-			}
+			return this.mapHashPeptide.get(temp);
 		}
-		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 {
@@ -14,28 +16,23 @@ public class HashProteinSet extends HashKey4GroupsSet {
 	 */
 	private static final Logger logger = Logger.getLogger(HashProteinSet.class);
 
+	private HashMap<HashProtein, HashProtein> mapHashProtein = new HashMap<HashProtein, HashProtein>(
+			0);
+
 	public HashProteinSet() {
 		// logger.debug("HashPeptideSet begin");
 	}
 
 	public HashProtein getInstance(String accession) {
 		HashProtein temp = new HashProtein(accession);
-
 		if (this.add(temp)) {
-			//this HashProtein is new
+			// this HashProtein is new
+			this.mapHashProtein.put(temp, temp);
 			return (temp);
+		} else {
+			// find the existing instance of the same protein :
+			return this.mapHashProtein.get(temp);
 		}
-		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

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

@@ -2,6 +2,7 @@ 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;
@@ -16,6 +17,8 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 	private static final long serialVersionUID = -9055338154900110371L;
 	private static final Logger logger = Logger
 			.getLogger(HashSampleScanSet.class);
+	private HashMap<HashSampleScan, HashSampleScan> mapHashSampleScan = new HashMap<HashSampleScan, HashSampleScan>(
+			0);
 
 	public HashSampleScanSet() {
 	}
@@ -31,19 +34,13 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 		HashSampleScan temp = new HashSampleScan(scan, msRun);
 
 		if (this.add(temp)) {
-			//this hashSampleScan is new
+			// this HashSampleScan is new
+			this.mapHashSampleScan.put(temp, temp);
 			return (temp);
-		}
-		else {
+		} else {
 			// find the existing instance of the same sample scan :
-			for (HashSampleScan toCompare:this) {
-				if (temp.equals(toCompare)) {
-					return toCompare;
-				}
-			}
+			return this.mapHashSampleScan.get(temp);
 		}
-		logger.error("ERROR this might not appear");
-		return temp;
 	}
 
 	public void loggerDebug() {