From f0c59406001ea5a0f92036a5808b9dccce6cb36d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 11 Jun 2017 22:34:49 +0200
Subject: [PATCH] WIP: mcqprm
---
src/output/masschroqprm.cpp | 141 ++++++++++++++++++------------------
1 file changed, 72 insertions(+), 69 deletions(-)
diff --git a/src/output/masschroqprm.cpp b/src/output/masschroqprm.cpp
index beecd71e..1bde93c9 100644
--- a/src/output/masschroqprm.cpp
+++ b/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()));
}
- }
+}
}
--
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