ODS phospho output OK

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

@@ -26,9 +26,12 @@ import java.util.Collection;
 import org.apache.log4j.Logger;
 
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
 import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
 import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
 import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpProtMatch;
 
 public class Utils {
 	private static final Logger logger = Logger.getLogger(Utils.class);
@@ -132,7 +135,8 @@ public class Utils {
 	}
 
 	public static String getPappsoPhosphoIslandId(Group group, SubGroup sg,
-			int k) throws MSMSException {
-		return getPappsoGroupingNumber(group, sg, k);
+			HashSampleScanSetPhospho phospho) throws MSMSException {
+		Protein prot = (Protein) phospho.getGrpProtMatch().getGrpProtein();
+		return getPappsoGroupingNumber(group, sg, prot.getPhosphoId());
 	}
 }

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

@@ -16,6 +16,8 @@ public class Protein implements GrpProtein {
 
 	private float mw;
 
+	private Integer phosphoId;
+
 	private int PAI_count;
 
 	private String description;
@@ -342,4 +344,34 @@ public class Protein implements GrpProtein {
 		return this.PAI_count;
 	}
 
+	/**
+	 * get the protein identifier of this protein usefull in the PhosphoIsland
+	 * context to get a unique PhosphoIsland ID
+	 * 
+	 * @return int
+	 * @throws MSMSException
+	 */
+	public int getPhosphoId() throws MSMSException {
+		if (this.phosphoId == null) {
+			String error = "phosphoId is null";
+			logger.debug(error);
+			throw new MSMSException(error);
+		}
+		return this.phosphoId.intValue();
+	}
+
+	/**
+	 * set the protein identifier of this protein usefull in the PhosphoIsland
+	 * context to get a unique PhosphoIsland ID the developper MUST give an id
+	 * number for each protein of PhosphoIslands
+	 * 
+	 * @param i
+	 */
+	public void setPhosphoId(int i) {
+		if (this.phosphoId == null) {
+			this.phosphoId = i;
+		}
+
+	}
+
 }

src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoProteinOutput.java

@@ -36,6 +36,7 @@ import fr.inra.pappso.xtandempipeline.Utils;
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.Identification;
 import fr.inra.pappso.xtandempipeline.class_msms.Match;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
 import fr.inra.pappso.xtandempipeline.grouping.Group;
 import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
 import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
@@ -142,7 +143,11 @@ public class OdsPhosphoProteinOutput {
 					for (HashSampleScanSetProt hashProt : sg
 							.getHashSampleScanSetProtList()) {
 						k++;
-						this.writeOnePhosphoProtein(hashProt, group, sg, k);
+						Protein prot = (Protein) hashProt.getGrpProtMatch()
+								.getGrpProtein();
+						prot.setPhosphoId(k);
+						this.writeOnePhosphoProtein(
+								(HashSampleScanSetPhospho) hashProt, group, sg);
 					}
 				}
 			}
@@ -162,14 +167,13 @@ public class OdsPhosphoProteinOutput {
 		}
 	}
 
-	private void writeOnePhosphoProtein(HashSampleScanSetProt hashProt,
-			Group group, SubGroup sg, int k) throws MSMSException {
+	private void writeOnePhosphoProtein(HashSampleScanSetPhospho phospho,
+			Group group, SubGroup sg) throws MSMSException {
 		try {
 			logger.debug("writeOnePhosphoProtein begin " + group + sg);
 			odsTable.writeLine();
 
-			Match top = (Match) hashProt.getGrpProtMatch();
-			HashSampleScanSetPhospho phospho = (HashSampleScanSetPhospho) hashProt;
+			Match top = (Match) phospho.getGrpProtMatch();
 
 			// odsTable.writeCell("Group ID");
 			odsTable.writeCell(Utils.getPappsoGroupId(group));
@@ -178,7 +182,8 @@ public class OdsPhosphoProteinOutput {
 			odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
 
 			// odsTable.writeCell("Phosphosite ID");
-			odsTable.writeCell(Utils.getPappsoPhosphoIslandId(group, sg, k));
+			odsTable.writeCell(Utils.getPappsoPhosphoIslandId(group, sg,
+					phospho));
 
 			// odsTable.writeCell("Description");
 			odsTable.writeCell(top.get_protein_match().get_description());

src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPhosphoSpectraOutput.java

@@ -162,8 +162,13 @@ public class OdsPhosphoSpectraOutput {
 					HashMap<PeptideMass, HashSet<Peptide>> hashPeptideMass2Peptides = new HashMap<PeptideMass, HashSet<Peptide>>();
 					int nbpeptide = 0;
 
+					int k = 0;
 					for (HashSampleScanSetProt hashPhospho : sg
 							.getHashSampleScanSetProtSet()) {
+						k++;
+						Protein prot = (Protein) hashPhospho.getGrpProtMatch()
+								.getGrpProtein();
+						prot.setPhosphoId(k);
 						for (Peptide peptide : ((Match) hashPhospho
 								.getGrpProtMatch())
 								.getValidPeptideInPhosphoIsland((HashSampleScanSetPhospho) hashPhospho)) {
@@ -195,10 +200,11 @@ public class OdsPhosphoSpectraOutput {
 					logger.debug("pepMassSet numbering");
 					pepMassSet.numbering();
 
+					HashSet<HashSampleScan> uniqueHashSampleScan = new HashSet<HashSampleScan>();
+
 					for (HashSampleScanSetProt hashPprot : sg
 							.getHashSampleScanSetProtSet()) {
 						HashSampleScanSetPhospho hashPhospho = (HashSampleScanSetPhospho) hashPprot;
-						HashSet<HashSampleScan> uniqueHashSampleScan = new HashSet<HashSampleScan>();
 
 						Protein prot = (Protein) hashPhospho.getGrpProtMatch()
 								.getGrpProtein();
@@ -326,12 +332,11 @@ public class OdsPhosphoSpectraOutput {
 			HashSet<HashSampleScanSetProt> phosphoIslandList = sg
 					.getHashSampleScanSetProtSet();
 			Collection<String> phosphoIslandsIds = new TreeSet<String>();
-			int k = 0;
+
 			for (HashSampleScanSetProt hashProt : phosphoIslandList) {
 				HashSampleScanSetPhospho phosphoIsland = (HashSampleScanSetPhospho) hashProt;
-				k++;
 				phosphoIslandsIds.add(Utils.getPappsoPhosphoIslandId(group, sg,
-						k));
+						phosphoIsland));
 			}
 			// odsTable.writeCell("Number of subgroups");
 			odsTable.writeCell(phosphoIslandsIds.size());

src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java

@@ -29,7 +29,7 @@ public class Mascot {
 
 	private MascotDatfile mascotDatfile;
 
-	//private Peptide peptide;
+	// private Peptide peptide;
 
 	private Protein prot_;
 
@@ -102,18 +102,16 @@ public class Mascot {
 
 	protected void addPeptideToIdentification(PeptideHit pep, Query query,
 			boolean reversed) throws MSMSException {
-		
+
 		// mapping proteinHit to protein && peptideHit to peptide
 		for (Object obj : pep.getProteinHits()) {
 			ProteinHit prot = (ProteinHit) obj;
-			
-			
-			//peptide = PeptideStore.getInstance().newPeptide();
+
+			// peptide = PeptideStore.getInstance().newPeptide();
 			Peptide pep_ = PeptideStore.getInstance().newPeptide();
 
 			pep_.set_sample_id(
-					identification_.getMsRunSet()
-							.getInstance(sample_), sample_);
+					identification_.getMsRunSet().getInstance(sample_), sample_);
 
 			pep_.set_charge((int) round(
 					(pep.getPeptideMr() / query.getPrecursorMZ()), 0));
@@ -123,14 +121,14 @@ public class Mascot {
 					+ pep.getDeltaMass() + 1.007825));
 			pep_.set_mhplus_theo((float) (pep.getPeptideMr() + 1.007825));
 			pep_.set_sequence(pep.getSequence());
-			
 
-			if(XtandemPipelineSession.getInstance().getConfig().get_mascot_evalue_theoritical()){
-				//Evalue theoritical
+			if (XtandemPipelineSession.getInstance().getConfig()
+					.get_mascot_evalue_theoritical()) {
+				// Evalue theoritical
 				pep_.set_evalue((float) pep.getExpectancy());
-			}else{
-				//Evalue experimental
-				double eval = (pep.getIonsScore()-pep.getHomologyThreshold())/10;
+			} else {
+				// Evalue experimental
+				double eval = (pep.getIonsScore() - pep.getHomologyThreshold()) / 10;
 				eval = 0.05 / Math.pow(10, eval);
 				pep_.set_evalue((float) eval);
 			}
@@ -180,7 +178,7 @@ public class Mascot {
 			// modified posi in prot of the peptide
 			pep_.set_start(prot.getStart());
 			pep_.set_stop(prot.getStop());
-			
+
 			// modifs add with position in prot!!!
 			Modification[] mods = pep.getModifications();
 			for (int i = 0; i < mods.length; i++) {
@@ -194,7 +192,7 @@ public class Mascot {
 					posi--;
 				}
 				if (mod != null) {
-					pep_.set_Modifs(mod.getLocation(), posi+prot.getStart(),
+					pep_.set_Modifs(mod.getLocation(), posi + prot.getStart(),
 							(float) mod.getMass());
 					identification_.add_modifs_to_liste(new Modifs((float) mod
 							.getMass()));

src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java

@@ -172,8 +172,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
 			pep_ = peptide;
 			// valeur généric du scan
 			try {
-				pep_.set_sample_id(identification_.getMsRunSet().getInstance(
-						sample_), sample_);
+				pep_.set_sample_id(
+						identification_.getMsRunSet().getInstance(sample_),
+						sample_);
 			} catch (MSMSException e) {
 				throw new SAXException(e);
 			}
@@ -202,9 +203,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
 				this.peptide = PeptideStore.getInstance().newPeptide();
 			}
 			pep_ = peptide;
-			pep_.set_Modifs(attrs.getValue("type"), Integer.parseInt(attrs
-					.getValue("at")), Float.valueOf(attrs.getValue("modified"))
-					.floatValue());
+			pep_.set_Modifs(attrs.getValue("type"),
+					Integer.parseInt(attrs.getValue("at")),
+					Float.valueOf(attrs.getValue("modified")).floatValue());
 			// modifs liste for isotopic analysis
 			identification_.add_modifs_to_liste(new Modifs(Float.valueOf(
 					attrs.getValue("modified")).floatValue()));
@@ -232,8 +233,9 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
 						match_ = (Match) identification_.get_match(prot_);
 						prot_ = match_.get_protein_match();
 					}
-					prot_.set_evalue(identification_.getMsRunSet().getInstance(
-							sample_), Float.valueOf(_evalue_prot).floatValue());
+					prot_.set_evalue(
+							identification_.getMsRunSet().getInstance(sample_),
+							Float.valueOf(_evalue_prot).floatValue());
 				}
 				if (spectre_number) {
 					String tmp = C_data.replaceAll(" ", "");

src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java

@@ -168,8 +168,9 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
 			}
 			pep_ = this.peptide;
 			try {
-				pep_.set_sample_id(identification_.getMsRunSet().getInstance(
-						sample_), sample_);
+				pep_.set_sample_id(
+						identification_.getMsRunSet().getInstance(sample_),
+						sample_);
 			} catch (MSMSException e) {
 				throw new SAXException(e);
 			}
@@ -198,9 +199,9 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
 				this.peptide = PeptideStore.getInstance().newPeptide();
 			}
 			pep_ = peptide;
-			pep_.set_Modifs(attrs.getValue("type"), Integer.parseInt(attrs
-					.getValue("at")), Float.valueOf(attrs.getValue("modified"))
-					.floatValue());
+			pep_.set_Modifs(attrs.getValue("type"),
+					Integer.parseInt(attrs.getValue("at")),
+					Float.valueOf(attrs.getValue("modified")).floatValue());
 			// modifs liste for isotopic analysis
 			identification_.add_modifs_to_liste(new Modifs(Float.valueOf(
 					attrs.getValue("modified")).floatValue()));
@@ -228,16 +229,20 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
 						match_ = (Match) identification_.get_match(prot_);
 						prot_ = match_.get_protein_match();
 					}
-					prot_.set_evalue(identification_.getMsRunSet().getInstance(
-							sample_), Float.valueOf(_evalue_prot).floatValue());
+					prot_.set_evalue(
+							identification_.getMsRunSet().getInstance(sample_),
+							Float.valueOf(_evalue_prot).floatValue());
 				}
 				if (spectre_number) {
 					String tmp = C_data.replaceAll(" .*", "");
 					String[] split = tmp.split("-");
 					if (split.length == 2) {
 						try {
-							int scan = Integer.parseInt(split[0].replaceAll("ScanNumber:", ""));
-							float rtime = Float.valueOf(split[1].replaceAll("RtInSec:", "")).floatValue();
+							int scan = Integer.parseInt(split[0].replaceAll(
+									"ScanNumber:", ""));
+							float rtime = Float.valueOf(
+									split[1].replaceAll("RtInSec:", ""))
+									.floatValue();
 							correction_scan.put("" + _scan, "" + scan);
 							correction_time.put("" + scan, "" + rtime);
 							logger.debug("" + scan + " = " + rtime);