Debugging peptide order!!!

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@80 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java

@@ -36,17 +36,17 @@ public class XtandemPipelineMain {
 	public static void main(String[] args) {
 		
 		//Chargement en debug mode
-		PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.properties"));
+//		PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.properties"));
 		//Chargement en release mode
-//		if(System.getProperty("os.name").contains("Linux")){
-//			PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.linux.properties"));
-//			logger.info("Linux logging");
-//			System.out.print("Linux logging");
-//		}else{
-//			PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.windows.properties"));
-//			logger.info("Window logging");
-//			System.out.print("Linux logging");
-//		}
+		if(System.getProperty("os.name").contains("Linux")){
+			PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.linux.properties"));
+			logger.info("Linux logging");
+			System.out.print("Linux logging");
+		}else{
+			PropertyConfigurator.configure(XtandemPipelineMain.class.getResource("/conf/log4j.windows.properties"));
+			logger.info("Window logging");
+			System.out.print("Linux logging");
+		}
 		logger.info("Starting new main");
 		new Main_Windows();
 		

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

@@ -5,6 +5,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import org.apache.log4j.Logger;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.filter_print.filter_base;
 import fr.inra.pappso.xtandempipeline.filter_print.print_base;
 import fr.inra.pappso.xtandempipeline.filter_print.swt_table_base;
@@ -102,7 +103,7 @@ public class Identification {
 		}
 	}
 
-	public void filtered_match(filter_base filter) {
+	public void filtered_match(filter_base filter) throws MSMSException {
 		int valid = filter.execute(this.protein_liste);
 		logger.info("Number of Valid Match " + valid);
 	}

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

@@ -7,6 +7,7 @@ import java.util.HashSet;
 
 import org.apache.log4j.Logger;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.grouping.HashProtein;
 import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
 import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
@@ -53,12 +54,17 @@ public class Match implements Comparable<Match> {
 		this.peptides_order.add(P);
 	}
 
-	public void IndexAndOrderPeptideListe() {
+	public void IndexAndOrderPeptideListe() throws MSMSException  {
 		this.peptides_match.clear();
 		Collections.sort(peptides_order);
 		for (Peptide pep : peptides_order) {
-			if (!this.peptides_match.containsKey(pep.getHashSampleScan()))
+			if (!this.peptides_match.containsKey(pep.getHashSampleScan())){
 				this.peptides_match.put(pep.getHashSampleScan(), pep);
+			}else{
+				if(this.peptides_match.get(pep.getHashSampleScan()).get_evalue()>pep.get_evalue()){
+					throw new MSMSException("OUPS problems of peptide order"+pep.get_sample_scan_sequencepeptide_cle());
+				}
+			}
 		}
 	}
 
@@ -250,7 +256,7 @@ public class Match implements Comparable<Match> {
 		return phosphoSiteList;
 	}
 
-	public Peptide getBestPeptideToHashSampleScan(HashSampleScan hash) {
+	public Peptide getBestPeptideToHashSampleScan(HashSampleScan hash) throws MSMSException {
 		Peptide pep = this.peptides_match.get(hash);
 		if(pep == null){
 			logger.error("Hastable of peptide is not indexed");

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

@@ -56,7 +56,14 @@ public class Peptide implements Comparable<Peptide> {
 		int i = this.hashSampleScan.compareTo(p.getSampleScan());
 		if (i != 0)
 			return (i);
-		return (int) (this.evalue - p.get_evalue());
+		float delta = this.evalue - p.get_evalue();
+		if(delta>0){
+			return(1);
+		}else if(delta<0){
+			return(-1);
+		}else{
+			return(0);
+		}
 	}
 
 	// constructeur

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

@@ -9,7 +9,7 @@ import org.apache.log4j.Logger;
 import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
 import fr.inra.pappso.xtandempipeline.grouping.HashProtein;
 
-public class Protein {
+public class Protein implements Comparable<Protein>{
 	private static final Logger logger = Logger.getLogger(Protein.class);
 
 	private float mw;
@@ -285,7 +285,8 @@ public class Protein {
 	public void set_peptide_number(int peptide_number) {
 		this.peptide_numbers = peptide_number;
 	}
-
+	
+@Override
 	public int compareTo(Protein prot) {	
 		return (this.get_cle_accession().compareTo(prot.get_cle_accession()));
 	}

xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_base.java

@@ -2,6 +2,7 @@ package fr.inra.pappso.xtandempipeline.filter_print;
 
 import org.apache.log4j.Logger;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.MatchList;
 
 public abstract class filter_base {
@@ -13,7 +14,7 @@ public abstract class filter_base {
 	public filter_base(){
 	}
 	
-	public int execute(MatchList m){
+	public int execute(MatchList m) throws MSMSException{
 		//processing de la match_list
 		return(numberOfValidMatch);
 	}

xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_index_and_order_match_scan.java

 package fr.inra.pappso.xtandempipeline.filter_print;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.Match;
 import fr.inra.pappso.xtandempipeline.class_msms.MatchList;
 
@@ -10,7 +11,7 @@ public class filter_index_and_order_match_scan extends filter_base {
 		logger.info("Index and order peptide liste in match");
 	}
 
-	public int execute(MatchList ms) {
+	public int execute(MatchList ms) throws MSMSException{
 		// processing de la match_list
 		for(Match m : ms.getMatchListes()){
 			m.IndexAndOrderPeptideListe();

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

@@ -4,6 +4,7 @@ import java.util.HashSet;
 
 import org.apache.log4j.Logger;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
 
 public class Group extends HashKey4GroupsSet implements Comparable<Group> {
@@ -294,7 +295,7 @@ public class Group extends HashKey4GroupsSet implements Comparable<Group> {
 	}
 
 	public int getNumberOfSpecificUniquePeptideInSubGroup(
-			HashSampleScanSetProt hashProt) {
+			HashSampleScanSetProt hashProt) throws MSMSException {
 		HashSet<String> sequences = new HashSet<String>();
 		for (HashSampleScan hash : hashProt) {
 			int view = 0;

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

 package fr.inra.pappso.xtandempipeline.grouping;
 
 import java.util.HashMap;
-import java.util.HashSet;
-import java.util.TreeSet;
 
 import org.apache.log4j.Logger;
 

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

@@ -5,6 +5,7 @@ import java.util.TreeSet;
 
 import org.apache.log4j.Logger;
 
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.Match;
 import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
 import fr.inra.pappso.xtandempipeline.class_msms.Peptide;
@@ -71,7 +72,7 @@ public class HashSampleScanSetPhospho extends HashSampleScanSetProt {
 		return(S);
 	}
 	
-	public boolean haveMultiPhosphoPeptide(){
+	public boolean haveMultiPhosphoPeptide() throws MSMSException{
 		boolean multi = false;
 		for(HashSampleScan hash: this){
 			if(this.match.getBestPeptideToHashSampleScan(hash).get_phospho_Modifs().size()>1)

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;
@@ -107,7 +106,7 @@ public class HashSampleScanSetProt extends HashSampleScanSet {
 		return hashPeptideSet;
 	}
 
-	public int getUniquePeptideHashSampleScan() {
+	public int getUniquePeptideHashSampleScan() throws MSMSException {
 		HashSet<String> sequence = new HashSet<String>();
 		for (HashSampleScan hash : this) {
 			Peptide pep = this.match.getBestPeptideToHashSampleScan(hash);
@@ -129,7 +128,7 @@ public class HashSampleScanSetProt extends HashSampleScanSet {
 		return (count);
 	}
 
-	public int getUniqueHashPeptideSampleScantoMsRun(MsRun sample) {
+	public int getUniqueHashPeptideSampleScantoMsRun(MsRun sample) throws MSMSException {
 		HashSet<String> sequence = new HashSet<String>();
 		for (HashSampleScan hash : this) {
 			Peptide pep = this.match.getBestPeptideToHashSampleScan(hash);