new xpip file format

src/output/xpip.cpp

+/**
+ * \file output/xpip.cpp
+ * \date 13/4/2017
+ * \author Olivier Langella
+ * \brief XPIP 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 "xpip.h"
+#include <pappsomspp/pappsoexception.h>
+
+Xpip::Xpip(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 XPIP output file : %1\n").arg(out_filename));
+    }
+
+    _output_stream->setAutoFormatting(true);
+    _output_stream->writeStartDocument("1.0");
+
+
+}
+
+Xpip::~Xpip()
+{
+    delete _output_file;
+    delete _output_stream;
+}
+
+void Xpip::close() {
+    _output_stream->writeEndDocument();
+    _output_file->close();
+}
+
+void Xpip::write(ProjectSp sp_project) {
+
+    _sp_project = sp_project;
+    if (_sp_project.get() == nullptr) {
+        throw pappso::PappsoException(QObject::tr("Error writing XPIP :\n project is empty"));
+    }
+
+//<xtandem_pipeline version="3.3.5">
+    _output_stream->writeStartElement("xpip");
+    _output_stream->writeAttribute("version","4.0");
+    //_output_stream->writeAttribute("creationDate", QDateTime::currentDateTime().toString( Qt::ISODate));
+    _output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
+    //_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
+    _output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/xpip/4.0");
+    //xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd"
+    _output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/xpip/4.0 http://pappso.inra.fr/xsd/xpip-4.0.xsd");
+
+    
+  //<information Data_Type="combi" match_number="6807"/>
+   // _output_stream->writeStartElement("information");
+  //  _output_stream->writeAttribute("Data_Type","combi");
+   // _output_stream->writeEndElement();
+    
+  //<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2" filter_to_all="false" database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
+    _output_stream->writeStartElement("filter_params");
+    _output_stream->writeAttribute("pep_evalue","combi");
+    _output_stream->writeAttribute("prot_evalue","combi");
+    _output_stream->writeAttribute("pep_number","combi");
+    _output_stream->writeAttribute("filter_to_all","combi");
+    _output_stream->writeEndElement();
+    
+  <identifications>
+    <identification>
+      <modifs_list_mass>
+        <modifs_mass modvalue="-18.01056"/>
+        <modifs_mass modvalue="-17.02655"/>
+        <modifs_mass modvalue="15.99491"/>
+        <modifs_mass modvalue="42.01057"/>
+        <modifs_mass modvalue="42.01056"/>
+        <modifs_mass modvalue="57.02146"/>
+      </modifs_list_mass>
+      <samples>
+        <sample value="20120906_balliau_extract_1_A01_urnb-1"/>
+        <sample value="20120906_balliau_extract_1_A02_urzb-1"/>
+      </samples>
+    //<masschroq>
+    // <rawdata><!-- time_values_dir="directory" to read retention time corrections-->
+    _output_stream->writeStartElement("rawdata");
+    _output_stream->writeComment("time_values_dir=\"directory\" to read retention time corrections");
+
+    std::vector<MsRunSp> msrun_list = _sp_project.get()->getMsRunStore().getMsRunList();
+    for (MsRunSp & msrun : msrun_list) {
+
+        //<data_file id="samp0" format="mzxml" path="bsa1.mzXML" type="centroid" />
+        _output_stream->writeStartElement("data_file");
+        _output_stream->writeAttribute("id",msrun.get()->getXmlId());
+        if(msrun.get()->getMzFormat() == MzFormat::mzXML) {
+            _output_stream->writeAttribute("format","mzxml");
+        }
+        _output_stream->writeAttribute("path",msrun.get()->getFilename());
+        _output_stream->writeAttribute("type","centroid");
+        // <data_file id="samp1" format="mzxml" path="bsa2.mzXML" type="profile" />
+        _output_stream->writeEndElement();
+    }
+    // <data_file id="samp2" format="mzml" path="/home/user/bsa3.mzml"      type="profile" />
+//<data_file id="samp3" format="mzml" path="/home/user/bsa4.mzml"             type="profile" />
+    // _output_stream.writeEndElement();
+    //             </rawdata>
+    _output_stream->writeEndElement();
+
+
+    writeGroups();
+    writeProteinList();
+    writePeptideList();
+    writeIsotopeLabelList();
+    writeAlignments();
+    writeQuantificationMethods();
+    _output_stream->writeStartElement("quantification");
+    writeQuantificationResults();
+    writeQuantificationTraces();
+    writeQuantify();
+    _output_stream->writeEndElement();
+}
+

src/output/xpip.h

+/**
+ * \file output/xpip.h
+ * \date 13/4/2017
+ * \author Olivier Langella
+ * \brief XPIP 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 XPIP_H
+#define XPIP_H
+
+#include <QXmlStreamWriter>
+#include <QFile>
+#include <QString>
+#include "../core/project.h"
+
+class Xpip
+{
+        public:
+    Xpip(const QString & out_filename);
+    ~Xpip();
+
+    void write(ProjectSp sp_project);
+    void close();
+  
+private :
+    QFile * _output_file;
+    QXmlStreamWriter * _output_stream;
+    ProjectSp _sp_project;
+
+};
+
+#endif // XPIP_H