trying to deal with fuzzy Brucker MGF

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

@@ -121,10 +121,17 @@ public class Mascot {
 					+ pep.getDeltaMass() + 1.007825));
 			pep_.set_mhplus_theo((float) (pep.getPeptideMr() + 1.007825));
 			pep_.set_sequence(pep.getSequence());
+<<<<<<< HEAD
 
 			if (XtandemPipelineSession.getInstance().getConfig()
 					.get_mascot_evalue_theoritical()) {
 				// Evalue theoritical
+=======
+			//query.getTitle();
+		
+			if(XtandemPipelineSession.getInstance().getConfig().get_mascot_evalue_theoritical()){
+				//Evalue theoritical
+>>>>>>> trying to deal with fuzzy Brucker MGF
 				pep_.set_evalue((float) pep.getExpectancy());
 			} else {
 				// Evalue experimental

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

@@ -168,9 +168,8 @@ 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);
 			}
@@ -199,9 +198,9 @@ 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()));
@@ -229,24 +228,39 @@ 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();
-							correction_scan.put("" + _scan, "" + scan);
-							correction_time.put("" + scan, "" + rtime);
-							logger.debug("" + scan + " = " + rtime);
-						} catch (Exception e) {
+					// example of X!tandem note on spectrum from mgf Bruker :
+					// <note label="Description">RTINSECONDS=769.441^M Cmpd
+					// 5568, +MSn(709.3404), 12.82 min MS: 5567/ MSMS: 5568/^M
+					// </note>
+					Pattern patt = Pattern
+							.compile("RTINSECONDS=([0-9.]+).*?MS: ([0-9]+)/ MSMS: ([0-9]+)");
+
+					Matcher m = patt.matcher(C_data.trim());
+					if (m.matches()) {
+						float rtime = Float.valueOf(m.group(1)).floatValue();
+						int scan = Integer.parseInt(m.group(3));
+						correction_scan.put("" + _scan, "" + scan);
+						correction_time.put("" + scan, "" + rtime);
+						logger.debug("Bruker MGF scan time fix " + scan + " = " + rtime);
+					} else {
+						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();
+								correction_scan.put("" + _scan, "" + scan);
+								correction_time.put("" + scan, "" + rtime);
+								logger.debug("" + scan + " = " + rtime);
+							} catch (Exception e) {
+							}
 						}
 					}
 					spectre_number = false;