files added for future masschroqprm writer

src/output/MassChroqPrmWriter.java

+/*******************************************************************************
+ * 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");
+	}
+
+}

src/output/masschroqprm.cpp

+/**
+ * \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()));
+    }
+	}
+
+}

src/output/masschroqprm.h

+/**
+ * \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