WIP: mcqprm

src/output/masschroqprm.cpp

@@ -72,76 +72,79 @@ void MassChroqPrm::write(ProjectSp sp_project) {
 
     //<masschroq>
     _output_stream->writeStartElement("masschroqprm");
+    /*
+    *
+    <parameters>
+    <parentIonMassTolerance>
+    <daltonPrecision value="1.5"/>
+    </parentIonMassTolerance>
+    <fragmentIonMassTolerance>
+    <daltonPrecision value="0.02"/>
+    </fragmentIonMassTolerance>
+    </parameters>
+     */
+    _output_stream->writeStartElement("parameters");
+    _output_stream->writeStartElement("parentIonMassTolerance");
+    _output_stream->writeComment("choose dalton or ppm mass precision to select parent ions based on the precursor mass of each MS/MS spectrum");
+    _output_stream->writeStartElement("ppmPrecision");
+    _output_stream->writeAttribute("value", "10");
+    _output_stream->writeEndElement();
+    _output_stream->writeEndElement();
+    _output_stream->writeStartElement("fragmentIonMassTolerance");
+    _output_stream->writeComment("choose dalton or ppm mass precision to MS/MS fragment ion observed mass with theoretical mass");
+    _output_stream->writeStartElement("daltonPrecision");
+    _output_stream->writeAttribute("value", "0.02");
+    _output_stream->writeEndElement();
+    _output_stream->writeEndElement();
+    _output_stream->writeEndElement();
+
+    writePeptides();
 }
 
-void MassChroqPrm::writePeptides(Identification ident) {
-		/*
-		 *
-		 *
-		 * <peptide seq="TCVADESHAGCEK" id="p1"> <psimod at="2"
-		 * acc="MOD:00397"/> <psimod at="11" acc="MOD:00397"/> </peptide>
-		 */
-		try {
-			/*
-			 *
-<parameters>
-<parentIonMassTolerance>
-	<daltonPrecision value="1.5"/>
-</parentIonMassTolerance>
-<fragmentIonMassTolerance>
-	<daltonPrecision value="0.02"/>
-</fragmentIonMassTolerance>
-</parameters>
-			 */
-			_output_stream->writeStartElement("parameters");
-			_output_stream->writeStartElement("parentIonMassTolerance");
-			_output_stream->writeComment("choose dalton or ppm mass precision to select parent ions based on the precursor mass of each MS/MS spectrum");
-			_output_stream->writeStartElement("ppmPrecision");
-			_output_stream->writeAttribute("value", "10");
-			_output_stream->writeEndElement();
-			_output_stream->writeEndElement();
-			_output_stream->writeStartElement("fragmentIonMassTolerance");
-			_output_stream->writeComment("choose dalton or ppm mass precision to MS/MS fragment ion observed mass with theoretical mass");
-			_output_stream->writeStartElement("daltonPrecision");
-			_output_stream->writeAttribute("value", "0.02");
-			_output_stream->writeEndElement();
-			_output_stream->writeEndElement();
-			_output_stream->writeEndElement();
-
-			_output_stream->writeStartElement("peptideList");
-
-			for (Group group : ident.getGrouping().getGroupList()) {
-				PeptideMassSet pepMassSet = new PeptideMassSet();
-
-				logger.debug("pepMassSet size : " + pepMassSet.size());
-
-				logger.debug("pepMassSet numbering");
-				pepMassSet.numberingGetPepMass2PeptideList(group);
-
-				// iterated current pepid to write buffer peptide element
-				for (PeptideMass pepMass : pepMassSet) {
-					_output_stream->writeStartElement("peptide");
-					_output_stream->writeAttribute("id",
-							Utils.getPappsoPeptideMassId(group, pepMass));
-					Peptide bestPeptide = pepMass.getBestEvaluePeptide();
-					_output_stream->writeAttribute("seq", bestPeptide.getSequence());
-
-					ArrayList<Modifs> arrModif = bestPeptide.get_Modifs();
-					for (Modifs modif : arrModif) {
-						_output_stream->writeStartElement("psimod");
-						_output_stream->writeAttribute("at", "" + modif.get_posi());
-
-						_output_stream->writeAttribute("acc", ""
-								+ modif.getPsiMod().getAccession());
-						_output_stream->writeEndElement();
-					}
-					_output_stream->writeEndElement();
-				}
-
-			}
-			_output_stream->writeEndElement();
-		} 
-		catch (pappso::PappsoException &error)
+void MassChroqPrm::writePeptides() {
+    /*
+     *
+     *
+     * <peptide seq="TCVADESHAGCEK" id="p1"> <psimod at="2"
+     * acc="MOD:00397"/> <psimod at="11" acc="MOD:00397"/> </peptide>
+     */
+    try {
+
+        _output_stream->writeStartElement("peptideList");
+
+        for (IdentificationGroup * p_ident_group : _sp_project.get()->getIdentificationGroupList()) {
+            for () {
+            PeptideMassSet pepMassSet = new PeptideMassSet();
+
+            logger.debug("pepMassSet size : " + pepMassSet.size());
+
+            logger.debug("pepMassSet numbering");
+            pepMassSet.numberingGetPepMass2PeptideList(group);
+
+            // iterated current pepid to write buffer peptide element
+            for (PeptideMass pepMass : pepMassSet) {
+                _output_stream->writeStartElement("peptide");
+                _output_stream->writeAttribute("id",
+                                               Utils.getPappsoPeptideMassId(group, pepMass));
+                Peptide bestPeptide = pepMass.getBestEvaluePeptide();
+                _output_stream->writeAttribute("seq", bestPeptide.getSequence());
+
+                ArrayList<Modifs> arrModif = bestPeptide.get_Modifs();
+                for (Modifs modif : arrModif) {
+                    _output_stream->writeStartElement("psimod");
+                    _output_stream->writeAttribute("at", "" + modif.get_posi());
+
+                    _output_stream->writeAttribute("acc", ""
+                                                   + modif.getPsiMod().getAccession());
+                    _output_stream->writeEndElement();
+                }
+                _output_stream->writeEndElement();
+            }
+
+        }
+        _output_stream->writeEndElement();
+    }
+    catch (pappso::PappsoException &error)
     {
         throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides :\n%1").arg(error.qwhat()));
     }
@@ -149,6 +152,6 @@ void MassChroqPrm::writePeptides(Identification ident) {
     {
         throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides stdex :\n%1").arg(error.what()));
     }
-	}
+}
 
 }