spectre output report modified to display proteins by subgroups

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

@@ -131,7 +131,7 @@ public class OdsComparPaiOutput {
 			odsTable.writeCell("Top Protein Description");
 			odsTable.writeCell("Number of proteins");
 
-			for (MsRun msSample : msSampleList) {
+			for (@SuppressWarnings("unused") MsRun msSample : msSampleList) {
 				odsTable.writeCell("PAI");
 				odsTable.writeCell("emPAI");
 			}

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

@@ -111,9 +111,10 @@ public class OdsComparSpectraOutput {
 
 			odsTable.writeLine();
 			odsTable.writeCell("Group ID");
+			odsTable.writeCell("Sub-group ID");
 			odsTable.writeCell("Top Protein ID");
 			odsTable.writeCell("Top Protein Description");
-			odsTable.writeCell("Number of subgroups");
+			odsTable.writeCell("Number of proteins");
 
 			MsRunSet msSampleList = ident.getMsRunSet();
 			msRunOrderedList = new TreeMap<String, MsRun>();
@@ -142,8 +143,10 @@ public class OdsComparSpectraOutput {
 
 			this.writeHeaders(ident);
 			for (Group group : ident.getGrouping().getGroupList()) {
-				this.writeOneGroup(ident, group);
-
+				// this.writeOneGroup(ident, group);
+				for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+					this.writeOneSubGroup(ident, group, sg);
+				}
 			}
 			odsTable.writeLine();
 			odsTable.writeLine();
@@ -161,24 +164,30 @@ public class OdsComparSpectraOutput {
 		}
 	}
 
-	private void writeOneGroup(Identification ident, Group group)
+	private void writeOneSubGroup(Identification ident, Group group, SubGroup sg)
 			throws MSMSException {
 		try {
-			logger.debug("writeOneGroup begin " + group);
+			logger.debug("writeOneSubGroup begin " + group);
+
+			// Match topMatch = (Match) sg.getHashSampleScanSetProtList().get(0)
+			// .getGrpProtMatch();
+
 			odsTable.writeLine();
 
 			// odsTable.writeCell("Group ID");
 			odsTable.writeCell(Utils.getPappsoGroupId(group));
 
-			SubGroup topSg = group.getSubGroupSet().getSubGroupList().get(0);
-			Protein topProt = (Protein) topSg.getHashSampleScanSetProtList()
+			// odsTable.writeCell("Sub-group ID");
+			odsTable.writeCell(Utils.getPappsoSubGroupId(group, sg));
+			Protein topProt = (Protein) sg.getHashSampleScanSetProtList()
 					.get(0).getGrpProtMatch().getGrpProtein();
 			// odsTable.writeCell("Top Protein ID");
-			odsTable.writeCell(Utils.getPappsoGroupingNumber(group, topSg, 1));
+			odsTable.writeCell(Utils.getPappsoGroupingNumber(group, sg, 1));
 			// odsTable.writeCell("Top Protein Description");
 			odsTable.writeCell(topProt.get_description());
-			// odsTable.writeCell("Number of subgroups");
-			odsTable.writeCell(group.getSubGroupSet().size());
+
+			// odsTable.writeCell("Number of proteins");
+			odsTable.writeCell(sg.getHashSampleScanSetProtList().size());
 
 			for (String msSampleName : msRunOrderedList.keySet()) {
 				odsTable.writeCell(group
@@ -186,16 +195,48 @@ public class OdsComparSpectraOutput {
 								.get(msSampleName)));
 			}
 
-			logger.debug("writeOneGroup end");
+			logger.debug("writeOneSubGroup end");
 		} catch (XMLStreamException e) {
-			String message = "XMLStreamException in writeOneGroup "
+			String message = "XMLStreamException in writeOneSubGroup "
 					+ e.getMessage();
 			logger.error(message);
 			throw new MSMSException(message);
 		} catch (Exception e) {
-			String message = "Exception in writeOneGroup " + e.getMessage();
+			String message = "Exception in writeOneSubGroup " + e.getMessage();
 			logger.error(message);
 			throw new MSMSException(message);
 		}
 	}
+
+	/*
+	 * private void writeOneGroup(Identification ident, Group group) throws
+	 * MSMSException { try { logger.debug("writeOneGroup begin " + group);
+	 * odsTable.writeLine();
+	 * 
+	 * // odsTable.writeCell("Group ID");
+	 * odsTable.writeCell(Utils.getPappsoGroupId(group));
+	 * 
+	 * SubGroup topSg = group.getSubGroupSet().getSubGroupList().get(0); Protein
+	 * topProt = (Protein) topSg.getHashSampleScanSetProtList()
+	 * .get(0).getGrpProtMatch().getGrpProtein(); //
+	 * odsTable.writeCell("Top Protein ID");
+	 * odsTable.writeCell(Utils.getPappsoGroupingNumber(group, topSg, 1)); //
+	 * odsTable.writeCell("Top Protein Description");
+	 * odsTable.writeCell(topProt.get_description()); //
+	 * odsTable.writeCell("Number of subgroups");
+	 * odsTable.writeCell(group.getSubGroupSet().size());
+	 * 
+	 * for (String msSampleName : msRunOrderedList.keySet()) {
+	 * odsTable.writeCell(group
+	 * .getNumberOfSpectraInGrpMsSample(msRunOrderedList .get(msSampleName))); }
+	 * 
+	 * logger.debug("writeOneGroup end"); } catch (XMLStreamException e) {
+	 * String message = "XMLStreamException in writeOneGroup " + e.getMessage();
+	 * logger.error(message); throw new MSMSException(message); } catch
+	 * (Exception e) { String message = "Exception in writeOneGroup " +
+	 * e.getMessage(); logger.error(message); throw new MSMSException(message);
+	 * }
+	 * 
+	 * }
+	 */
 }