clear function overrided on sets

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@72 b8ef2a07-7df7-436f-90b9-41648038564b

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

@@ -41,6 +41,11 @@ public class Match implements Comparable<Match> {
 		this.protein_match = new Protein();
 		this.isvalidate = true;
 	}
+	
+	@Override
+	protected void finalize() throws Throwable {
+		logger.debug("finalize Match");
+	}
 
 	public void add_peptide_match(Peptide P) {
 		// if (!this.peptides_match.containsKey(P.get_sample_scan_cle()))

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

@@ -2,6 +2,7 @@ package fr.inra.pappso.xtandempipeline.grouping;
 
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.TreeSet;
 
 import org.apache.log4j.Logger;
 
@@ -20,10 +21,17 @@ public class HashPeptideSet extends HashKey4GroupsSet {
 			0);
 
 	public HashPeptideSet() {
-		//logger.debug("HashPeptideSet begin");
+		// logger.debug("HashPeptideSet begin");
 	}
 
-	public HashPeptide getInstance(HashSampleScan sampleScan, String sequence) throws Exception {
+	@Override
+	public void clear() {
+		getHashPeptide = new HashMap<Integer, HashPeptide>(0);
+		super.clear();
+	}
+
+	public HashPeptide getInstance(HashSampleScan sampleScan, String sequence)
+			throws Exception {
 		if (sampleScan == null) {
 			throw new Exception("sampleScan is null");
 		}

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

@@ -20,7 +20,7 @@ public class HashProteinSet extends HashKey4GroupsSet {
 			0);
 
 	public HashProteinSet() {
-		//logger.debug("HashPeptideSet begin");
+		// logger.debug("HashPeptideSet begin");
 	}
 
 	public HashProtein getInstance(String accession) {
@@ -33,4 +33,10 @@ public class HashProteinSet extends HashKey4GroupsSet {
 		return getHashProtein.get(temp.hashCode());
 	}
 
+	@Override
+	public void clear() {
+		getHashProtein = new HashMap<Integer, HashProtein>(0);
+		super.clear();
+	}
+
 }

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

 package fr.inra.pappso.xtandempipeline.grouping;
 
+import org.apache.log4j.Logger;
+
 import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
 
 public class HashSampleScan implements Comparable<HashSampleScan> {
+	private static final Logger logger = Logger.getLogger(HashSampleScan.class);
+
 	private int scan;
 	private MsRun msRun;
 	private int hascode;
@@ -14,6 +18,11 @@ public class HashSampleScan implements Comparable<HashSampleScan> {
 		this.msRun = msRun;
 		this.hascode = this.getHashCodeStr().hashCode();
 	}
+	
+	@Override
+	protected void finalize() throws Throwable {
+		logger.debug("finalize HashSampleScan");
+	}
 
 	private String getHashCodeStr() {
 		String code;

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

@@ -28,7 +28,7 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 		int i = arg0.size() - this.size();
 		if (i != 0)
 			return i;
-		return (this.getFingerCode()-arg0.getFingerCode());
+		return (this.getFingerCode() - arg0.getFingerCode());
 	}
 
 	public HashSampleScan getInstance(int scan, MsRun msRun) {
@@ -48,34 +48,39 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
 		}
 		// return null;
 	}
-	
-	public ArrayList<HashSampleScan> getHashSampleScanList(){
+
+	public ArrayList<HashSampleScan> getHashSampleScanList() {
 		ArrayList<HashSampleScan> array = new ArrayList<HashSampleScan>(this);
 		Collections.sort(array);
-		return(array);
+		return (array);
 	}
-	
+
 	private int getFingerCode() {
 		int finger = 0;
-		for (HashSampleScan sampleScan:this) {
-			finger+=sampleScan.getScan();
+		for (HashSampleScan sampleScan : this) {
+			finger += sampleScan.getScan();
 		}
-		return(finger);
+		return (finger);
+	}
+
+	@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;
-//	}
 
+	// 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;
+	// }
 
 }

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

@@ -43,6 +43,13 @@ public class HashSampleScanSetPhospho extends HashSampleScanSetProt {
 
 	}
 
+	@Override
+	public void clear() {
+		phosphoPositions = new TreeSet<Integer>();
+		super.clear();
+	}
+
+
 	@Override
 	public int compareTo(HashSampleScanSet o) {
 		int i = o.size() - this.size();

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

 package fr.inra.pappso.xtandempipeline.grouping;
 
+import java.util.HashMap;
 import java.util.HashSet;
 
 import org.apache.log4j.Logger;
@@ -34,6 +35,12 @@ public class HashSampleScanSetProt extends HashSampleScanSet {
 		}
 	}
 
+	@Override
+	public void clear() {
+		match = null;
+		super.clear();
+	}
+
 	@Override
 	public String toString() {
 		return match.get_protein_match().get_cle_accession();