diff --git a/src/output/MassChroqPrmWriter.java b/src/output/MassChroqPrmWriter.java
new file mode 100644
index 0000000000000000000000000000000000000000..50b3815b06be1e0f12a84e3938c706885bf4412e
--- /dev/null
+++ b/src/output/MassChroqPrmWriter.java
@@ -0,0 +1,182 @@
+/*******************************************************************************
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTandemPipeline.
+ *
+ * XTandemPipeline is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTandemPipeline is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTandemPipeline. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr>
+ ******************************************************************************/
+
+package fr.inra.pappso.xtandempipeline.output;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamWriter;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.moulon.proticport.model.exceptions.ProticPortException;
+import fr.inra.pappso.xtandempipeline.Utils;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
+import fr.inra.pappso.xtandempipeline.class_msms.ModifsList;
+import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
+import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
+import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMassSet;
+import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
+import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSet;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
+import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPeptide;
+
+public class MassChroqPrmWriter {
+ private static final Logger logger = Logger
+ .getLogger(MassChroqPrmWriter.class);
+
+ static String namespaceURI = "http://sashimi.sourceforge.net/schema_revision/mzXML_2.0";
+ static String xmlnsxsi = "http://www.w3.org/2001/XMLSchema-instance";
+ static String xsischemaLocation = "http://sashimi.sourceforge.net/schema_revision/mzXML_2.0 http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/mzXML_idx_2.0.xsd";
+
+ protected XMLStreamWriter writer;
+
+ private Hashtable<MsRun, String> sample2xmlId;
+ private String groupe_id;
+
+ private String xtpExperimentType;
+
+ private Hashtable<String, String> accession2xmlid;
+
+ MassChroqPrmWriter(XMLStreamWriter writer) throws ProticPortException {
+ this.sample2xmlId = new Hashtable<MsRun, String>();
+ this.groupe_id = "G1";
+ this.writer = writer;
+
+ }
+
+ public void write(ModifsList isotopic_mods, Identification ident)
+ throws XMLStreamException, ProticPortException {
+ logger.debug("write begin");
+ long duracel = System.currentTimeMillis();
+
+ xtpExperimentType = XtandemPipelineSession.getInstance()
+ .getDataTypeBase().getType();
+
+ if (this.xtpExperimentType.equals("phospho")) {
+ accession2xmlid = new Hashtable<String, String>();
+ }
+
+ // writer.setPrefix("xsi", xmlnsxsi);
+ // writer.setDefaultNamespace(namespaceURI);
+ writer.writeStartElement("masschroqprm");
+ // writer.writeNamespace("xsi", xmlnsxsi);
+ // writer.writeDefaultNamespace(namespaceURI);
+
+ // writer.writeAttribute(xmlnsxsi, "schemaLocation", xsischemaLocation);
+
+ this.writePeptides(ident);
+
+ logger.info("Duration creating MassChroQml xml document: "
+ + (System.currentTimeMillis() - duracel) + " ms");
+ // masschroq
+ writer.writeEndElement();
+
+ }
+
+ private void writePeptides(Identification ident) {
+ logger.debug("write begin");
+ /*
+ *
+ *
+ * <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>
+ */
+ writer.writeStartElement("parameters");
+ writer.writeStartElement("parentIonMassTolerance");
+ writer.writeComment("choose dalton or ppm mass precision to select parent ions based on the precursor mass of each MS/MS spectrum");
+ writer.writeStartElement("ppmPrecision");
+ writer.writeAttribute("value", "10");
+ writer.writeEndElement();
+ writer.writeEndElement();
+ writer.writeStartElement("fragmentIonMassTolerance");
+ writer.writeComment("choose dalton or ppm mass precision to MS/MS fragment ion observed mass with theoretical mass");
+ writer.writeStartElement("daltonPrecision");
+ writer.writeAttribute("value", "0.02");
+ writer.writeEndElement();
+ writer.writeEndElement();
+ writer.writeEndElement();
+
+ writer.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) {
+ writer.writeStartElement("peptide");
+ writer.writeAttribute("id",
+ Utils.getPappsoPeptideMassId(group, pepMass));
+ Peptide bestPeptide = pepMass.getBestEvaluePeptide();
+ writer.writeAttribute("seq", bestPeptide.getSequence());
+
+ ArrayList<Modifs> arrModif = bestPeptide.get_Modifs();
+ for (Modifs modif : arrModif) {
+ writer.writeStartElement("psimod");
+ writer.writeAttribute("at", "" + modif.get_posi());
+
+ writer.writeAttribute("acc", ""
+ + modif.getPsiMod().getAccession());
+ writer.writeEndElement();
+ }
+ writer.writeEndElement();
+ }
+
+ }
+ writer.writeEndElement();
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ }
+ logger.debug("write end");
+ }
+
+}
diff --git a/src/output/masschroqprm.cpp b/src/output/masschroqprm.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..beecd71e4f67eb23bf96783e8bc0d35214bff410
--- /dev/null
+++ b/src/output/masschroqprm.cpp
@@ -0,0 +1,154 @@
+/**
+ * \file output/masschroqprm.cpp
+ * \date 10/6/2017
+ * \author Olivier Langella
+ * \brief MassChroqPRM writer
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "masschroqprm.h"
+#include <pappsomspp/pappsoexception.h>
+
+MassChroqPrm::MassChroqPrm(const QString & out_filename) {
+ //_p_digestion_pipeline = p_digestion_pipeline;
+
+ //_mzidentml = "http://psidev.info/psi/pi/mzIdentML/1.1";
+ QString complete_out_filename = out_filename;
+ _output_file = new QFile(complete_out_filename);
+
+ if (_output_file->open(QIODevice::WriteOnly))
+ {
+ _output_stream = new QXmlStreamWriter();
+ _output_stream->setDevice(_output_file);
+ } else
+ {
+ throw pappso::PappsoException(QObject::tr("error : cannot open the MassChroqPRM output file : %1\n").arg(out_filename));
+ }
+
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
+
+
+}
+
+MassChroqPrm::~MassChroqPrm()
+{
+ delete _output_file;
+ delete _output_stream;
+}
+
+void MassChroqPrm::close() {
+ _output_stream->writeEndDocument();
+ _output_file->close();
+}
+
+void MassChroqPrm::write(ProjectSp sp_project) {
+
+ _sp_project = sp_project;
+ if (_sp_project.get() == nullptr) {
+ throw pappso::PappsoException(QObject::tr("Error writing MassChroqPRM file :\n project is empty"));
+ }
+
+ //<masschroq>
+ _output_stream->writeStartElement("masschroqprm");
+}
+
+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)
+ {
+ throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides :\n%1").arg(error.qwhat()));
+ }
+ catch (std::exception &error)
+ {
+ throw pappso::PappsoException(QObject::tr("Error in MassChroqPrm::writePeptides stdex :\n%1").arg(error.what()));
+ }
+ }
+
+}
diff --git a/src/output/masschroqprm.h b/src/output/masschroqprm.h
new file mode 100644
index 0000000000000000000000000000000000000000..31aca8f40a58ed9bb8b87089bc23da0a9f1b400b
--- /dev/null
+++ b/src/output/masschroqprm.h
@@ -0,0 +1,66 @@
+/**
+ * \file output/masschroqprm.h
+ * \date 10/6/2017
+ * \author Olivier Langella
+ * \brief MassChroqPRM writer
+ */
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef MASSCHROQPRM_H
+#define MASSCHROQPRM_H
+
+#include <QXmlStreamWriter>
+#include <QFile>
+#include <QString>
+#include "../core/project.h"
+#include "../grouping/groupinggroup.h"
+
+class MassChroqPrm
+{
+ public:
+ MassChroqPrm(const QString & out_filename);
+ ~MassChroqPrm();
+
+ void write(ProjectSp sp_project);
+ void close();
+private:
+ void writeGroups();
+ void writeProteinList();
+ void writePeptideList();
+ void writePeptideListInGroup(const GroupingGroup * p_group);
+ void writeIsotopeLabelList();
+ void writeAlignments();
+ void writeQuantificationMethods();
+ void writeQuantificationResults();
+ void writeQuantificationTraces();
+ void writeQuantify();
+
+private :
+ QFile * _output_file;
+ QXmlStreamWriter * _output_stream;
+ ProjectSp _sp_project;
+ IdentificationGroup * _p_identification_group;
+};
+
+#endif // MASSCHROQPRM_H