stores and reads scan number correspondance from XPIP files

src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationDataSource.java

@@ -32,11 +32,20 @@ public interface IdentificationDataSource extends
 	 * store scan number correspondance information
 	 * 
 	 * this is usefull in case the real scan num (given by the spectrometer) is
-	 * not the same as indicated in the identification data source :
-	 * one can store the fuzzy scan number and still can get MSMS data from the source
+	 * not the same as indicated in the identification data source : one can
+	 * store the fuzzy scan number and still can get MSMS data from the source
 	 * 
 	 */
 	public void setScanCorrespondance(int fixedScanNum,
 			int scanNumAsWrittenInDataSource);
 
+	/**
+	 * gets the identifier of the spectrum within this datasource, given the
+	 * real spectrum scan number
+	 * 
+	 * @param scanNumber
+	 * @return NULL if there is no correspondance
+	 */
+	public Integer getScanCorrespondance(int scanNumber);
+
 }

src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationMascotFile.java

@@ -56,4 +56,9 @@ public class IdentificationMascotFile extends IdentificationDataFile {
 			int scanNumAsWrittenInDataSource) {
 
 	}
+
+	@Override
+	public Integer getScanCorrespondance(int scanNumber) {
+		return null;
+	}
 }

src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationProticPortSource.java

@@ -123,4 +123,9 @@ public class IdentificationProticPortSource implements IdentificationDataSource
 			int scanNumAsWrittenInDataSource) {
 
 	}
+
+	@Override
+	public Integer getScanCorrespondance(int scanNumber) {
+		return null;
+	}
 }

src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java

@@ -110,9 +110,16 @@ public class IdentificationXtandemFile extends IdentificationDataFile {
 	@Override
 	public void setScanCorrespondance(int fixedScanNum,
 			int scanNumAsWrittenInDataSource) {
+		if (fixedScanNum == scanNumAsWrittenInDataSource)
+			return;
 		logger.debug("setScanCorrespondance " + fixedScanNum + "=>"
 				+ scanNumAsWrittenInDataSource);
 		this.scanNum2XtandemScanNum.put(fixedScanNum,
 				scanNumAsWrittenInDataSource);
 	}
+
+	@Override
+	public Integer getScanCorrespondance(int scanNumber) {
+		return scanNum2XtandemScanNum.get(scanNumber);
+	}
 }

src/fr/inra/pappso/xtandempipeline/output/XpipWriter.java

@@ -15,6 +15,7 @@ import fr.inra.pappso.xtandempipeline.class_msms.Identification;
 import fr.inra.pappso.xtandempipeline.class_msms.Match;
 import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
 import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataSource;
 import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
 import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
 import fr.inra.pappso.xtandempipeline.thread.process;
@@ -108,10 +109,15 @@ public class XpipWriter {
 	private void write_peptide_to(Peptide pep) throws Exception {
 		writer.writeStartElement("peptide");
 		writer.writeAttribute("sample", pep.get_sample());
-		pep.getIdentificationDataSource().writeXpipPeptideSourceAttribute(
-				writer);
+		IdentificationDataSource dataSource = pep.getIdentificationDataSource();
+		dataSource.writeXpipPeptideSourceAttribute(writer);
 		writer.writeAttribute("scan", "" + pep.get_scan());
-		writer.writeAttribute("scan_in_xtandem", "" + pep.get_scan());
+
+		Integer scanCorrespondance = dataSource.getScanCorrespondance(pep
+				.get_scan());
+		if (scanCorrespondance != null) {
+			writer.writeAttribute("scan_in_xtandem", "" + scanCorrespondance);
+		}
 		writer.writeAttribute("RT", "" + pep.get_RT_in_sec());
 		writer.writeAttribute("mhplus_obser", "" + pep.get_mhplus_obser());
 		writer.writeAttribute("mhplus_theo", "" + pep.get_mhplus_theo());

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

@@ -138,9 +138,9 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
 				if (sampleName == null) {
 					throw new MSMSException("sample attribute is null");
 				}
-				prot_.set_evalue(identification_.getMsRunSet().getInstance(
-						sampleName), Float.valueOf(attrs.getValue("evalue"))
-						.floatValue());
+				prot_.set_evalue(
+						identification_.getMsRunSet().getInstance(sampleName),
+						Float.valueOf(attrs.getValue("evalue")).floatValue());
 			}
 			if (Start_element_.equals("peptide")) {
 				this.startElementpeptide(namespaceURI, attrs);
@@ -235,16 +235,19 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
 							originalFileName);
 			peptide.set_sample_id(this.identification_.getMsRunSet()
 					.getInstance(sampleName), sample_file);
-			if (attrs.getValue("scan_in_xtandem") == null) {
-				throw new MSMSException("scan_in_xtandem is null");
-			}
-			logger.debug("peptide.set_scan");
-			peptide.set_scan(Integer
-					.parseInt(attrs.getValue("scan_in_xtandem")));
+
+			//read scan number :
 			if (attrs.getValue("scan") == null) {
 				throw new MSMSException("scan is null");
 			}
 			peptide.set_scan(Integer.parseInt(attrs.getValue("scan")));
+			if (attrs.getValue("scan_in_xtandem") != null) {
+				//if there is a correspondance to make in the source file :
+				sample_file.setScanCorrespondance(peptide.get_scan(),
+						Integer.parseInt(attrs.getValue("scan_in_xtandem")));
+			}
+			
+
 			if (attrs.getValue("RT") == null) {
 				// throw new MSMSException("RT is null");
 				logger.warn("RT is null");
@@ -371,8 +374,8 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
 			prot_ = null;
 		}
 		if (Last_element_.equals("identification")) {
-			XtandemPipelineSession.getInstance().getIdentificationList().add(
-					identification_);
+			XtandemPipelineSession.getInstance().getIdentificationList()
+					.add(identification_);
 		}
 		C_data = "";
 	}