first attempt to fix Brucker scan nums

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

@@ -121,17 +121,11 @@ 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

@@ -4,6 +4,8 @@ import org.apache.log4j.Logger;
 import org.xml.sax.*;
 import java.util.Hashtable;
 import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.class_msms.*;
@@ -52,6 +54,9 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
 
 	private boolean spectre_number;
 
+	private Pattern pattBruckerRtScanNum = Pattern
+			.compile("RTINSECONDS=([0-9]+.[0-9]+).*?MS: ([0-9]+)/ MSMS: ([0-9]+).*");
+
 	public xtandem(Identification L, IdentificationDataSource S) {
 		super();
 		if (L == null) {
@@ -168,8 +173,9 @@ 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 +204,9 @@ 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()));
@@ -228,25 +234,34 @@ 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) {
 					// 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());
+					// Pattern patt = Pattern
+					// .compile("RTINSECONDS=([0-9]+.[0-9]+).*?MS: ([0-9]+)/ MSMS: ([0-9]+)");
+					// Pattern patt = Pattern
+					// .compile("MS: ([0-9]+)\\/ MSMS: ([0-9]+)");
+					// Pattern patt = Pattern
+					// .compile("RTINSECONDS(.*)");
+					// logger.debug("C_data"+C_data.replace("\n",
+					// "").replace("\r", ""));
+					Matcher m = pattBruckerRtScanNum.matcher(C_data.replace(
+							"\n", "").replace("\r", ""));
 					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);
+						logger.debug("Bruker MGF scan time fix " + scan + " = "
+								+ rtime);
 					} else {
+						// logger.debug("no match");
 						String tmp = C_data.replaceAll(" .*", "");
 						String[] split = tmp.split("-");
 						if (split.length == 2) {