add X!Tandem hyperscore in the spectra output

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

@@ -40,7 +40,6 @@ 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.MsRun;
-import fr.inra.pappso.xtandempipeline.class_msms.Protein;
 import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
 import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMassSet;
 import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
@@ -128,6 +127,7 @@ public class OdsSpectraOutput {
 			odsTable.writeCell("Number of subgroups");
 			odsTable.writeCell("Sub-groups Ids");
 			odsTable.writeCell("Best E-value");
+			odsTable.writeCell("Best hyperscore");
 			odsTable.writeCell("Charge");
 			odsTable.writeCell("MH+ Obs");
 			odsTable.writeCell("MH+ theo");
@@ -238,8 +238,8 @@ public class OdsSpectraOutput {
 		try {
 			logger.debug("writeOneHashSampleScan begin " + group + pepMass);
 			MsRun msRun = (MsRun) scan.getGrpMsSample();
-			Protein prot = (Protein) hashSampleScanSetProt.getGrpProtMatch()
-					.getGrpProtein();
+			// Protein prot = (Protein) hashSampleScanSetProt.getGrpProtMatch()
+			// .getGrpProtein();
 			Peptide bestPeptide = null;
 			Collection<GrpPeptide> peptideList = hashSampleScanSetProt
 					.getGrpProtMatch().getGrpPeptides();
@@ -256,7 +256,7 @@ public class OdsSpectraOutput {
 				}
 			}
 			if (bestPeptide == null) {
-				//throw new MSMSException("bestPeptide == null");
+				// throw new MSMSException("bestPeptide == null");
 				return;
 			}
 			// Peptide bestPeptide = pepMass.getBestEvaluePeptide();
@@ -303,6 +303,9 @@ public class OdsSpectraOutput {
 			// odsTable.writeCell("Best E-value");
 			odsTable.writeCell(bestPeptide.get_evalue());
 
+			// odsTable.writeCell("Best hyperscore");
+			odsTable.writeCell(bestPeptide.get_hypercorr());
+
 			// odsTable.writeCell("Charge");
 			odsTable.writeCell(bestPeptide.get_charge());