diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9d83c28381795063e2aaf2c1413a7bf8b640d8bf..150a5ff3cc0d897026c2f2ccb048ca245c3e04b0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -71,6 +71,7 @@ SET(CPP_FILES
gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
input/xpipsaxhandler.cpp
input/xtandemsaxhandler.cpp
+ output/masschroqml.cpp
utils/identificationdatasourcestore.cpp
utils/groupstore.cpp
utils/msrunstore.cpp
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index f5685957b9625809884c9781f20e25d781a8f34f..38e7c45412eff029c20ef1eb67da290ffc4bfe20 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -61,3 +61,7 @@ const QString & MsRun::getXmlId() const {
const QString & MsRun::getFilename() const {
return _location;
}
+
+MzFormat MsRun::getMzFormat() const {
+ return _mz_format;
+}
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 5262b2bead094bfff276405ce12ac683491334eb..40604c926839d3297300452b3b05cabfee134014 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -34,6 +34,7 @@
#include <memory>
#include <QString>
+#include "../utils/types.h"
class MsRun;
typedef std::shared_ptr<MsRun> MsRunSp;
@@ -50,10 +51,13 @@ public:
const QString & getFilename() const;
const QString & getXmlId() const;
+
+ MzFormat getMzFormat() const;
private :
QString _xml_id;
QString _location;
QString _name;
+ MzFormat _mz_format=MzFormat::mzXML;
};
#endif // MSRUN_H
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 210b0e11c5c8f96a2bb61ee06ea109d0884c3276..0437c22e6ddcedb7006334894d7f776bccc7f511 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -122,12 +122,6 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
}
-IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
-
- qDebug() << "Project::getCurrentIdentificationGroupP begin " << _p_current_identification_group;
- return _p_current_identification_group;
-}
-
void Project::startGrouping() {
for (auto & p_id_group : _identification_goup_list) {
diff --git a/src/core/project.h b/src/core/project.h
index 3d04785b86604291452b4cc7f2594550feff9e7a..cbf721250a1cde53cc6ee525f730cebf96057a72 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -51,7 +51,6 @@ public:
IdentificationDataSourceStore & getIdentificationDataSourceStore();
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
- IdentificationGroup* getCurrentIdentificationGroupP() const;
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
diff --git a/src/gui/main.ui b/src/gui/main.ui
index 8c36b0b947867c06150e1f9cff2893583573db34..4fd14c2e2d57770d32a465baba4cf79719a082c9 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -26,15 +26,25 @@
<x>0</x>
<y>0</y>
<width>463</width>
- <height>23</height>
+ <height>25</height>
</rect>
</property>
<widget class="QMenu" name="menuFile">
<property name="title">
<string>F&ile</string>
</property>
+ <widget class="QMenu" name="menuExport_files">
+ <property name="title">
+ <string>Export files</string>
+ </property>
+ <addaction name="actionFasta"/>
+ <addaction name="actionMassChroQ"/>
+ <addaction name="actionSpreadsheet"/>
+ </widget>
<addaction name="actionLoad_results"/>
<addaction name="actionLoad"/>
+ <addaction name="separator"/>
+ <addaction name="menuExport_files"/>
</widget>
<addaction name="menuFile"/>
</widget>
@@ -46,7 +56,22 @@
</action>
<action name="actionLoad_results">
<property name="text">
- <string>Load results</string>
+ <string>Load &results</string>
+ </property>
+ </action>
+ <action name="actionFasta">
+ <property name="text">
+ <string>Fasta</string>
+ </property>
+ </action>
+ <action name="actionMassChroQ">
+ <property name="text">
+ <string>MassChroQ</string>
+ </property>
+ </action>
+ <action name="actionSpreadsheet">
+ <property name="text">
+ <string>Spreadsheet</string>
</property>
</action>
</widget>
@@ -86,9 +111,26 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>actionMassChroQ</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>doActionMassChroQ()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>231</x>
+ <y>191</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>selectXpipFile()</slot>
<slot>loadResults()</slot>
+ <slot>doActionMassChroQ()</slot>
</slots>
</ui>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 023c091235555831bfea48cd45cff6bb19741704..d4a10d9324fae909decbe0edafc4352563dc20d3 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -30,6 +30,7 @@
#include "ui_main.h"
#include <pappsomspp/pappsoexception.h>
+#include "../output/masschroqml.h"
void XtpLoaderThread::doXpipFileLoad(QString filename) {
@@ -37,7 +38,7 @@ void XtpLoaderThread::doXpipFileLoad(QString filename) {
try {
QFileInfo new_xpip_file;
new_xpip_file.setFile(filename);
-
+ emit loadingMessage(tr("loading XPIP file"));
XpipFile xpip_file(new_xpip_file);
ProjectSp project_sp = xpip_file.getProjectSp();
@@ -175,8 +176,10 @@ void MainWindow::doProjectReady(ProjectSp project_sp) {
qDebug() << "MainWindow::doProjectReady begin";
try {
+ _project_sp = project_sp;
doDisplayLoadingMessage(tr("grouping proteins"));
project_sp.get()->startGrouping();
+ doDisplayLoadingMessage(tr("grouping proteins finished"));
}
catch (pappso::PappsoException & error) {
viewError(tr("Error while grouping :\n%1").arg(error.qwhat()));
@@ -219,3 +222,27 @@ void MainWindow::selectXpipFile() {
}
+void MainWindow::doActionMassChroQ() {
+ qDebug() << "MainWindow::doActionMassChroQ begin";try {
+ QSettings settings;
+ QString default_location = settings.value("path/mcqfile", "").toString();
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save MassChroqML file"),
+ QString("%1/untitled.masschroqml").arg(default_location),
+ tr("MassChroqML (*.masschroqml)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+
+ settings.setValue("path/mcqfile", QFileInfo(filename).absolutePath());
+ MassChroQml output(filename);
+ output.write(_project_sp);
+ output.close();
+ //emit operateXpipFile(filename);
+ }
+ catch (pappso::PappsoException & error) {
+ viewError(tr("Error while writing MassChroqML file :\n%1").arg(error.qwhat()));
+ }
+ qDebug() << "MainWindow::doActionMassChroQ end";
+}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 43946b49ae262f35426e49c8afff5cb425080b3e..02eb1617a3f571ce551a56ea1d0d426e3a88218e 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -78,6 +78,7 @@ public:
public slots:
void loadResults();
void selectXpipFile();
+ void doActionMassChroQ();
void doDisplayLoadingMessage(QString message);
void doProjectReady(ProjectSp project_sp);
void doProjectNotReady(QString error);
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b4492759bbc8cd413e88dcd1fb86c8b4ef1647dc
--- /dev/null
+++ b/src/output/masschroqml.cpp
@@ -0,0 +1,188 @@
+/**
+ * \file output/masschroqml.cpp
+ * \date 7/4/2017
+ * \author Olivier Langella
+ * \brief MassChroQML 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 "masschroqml.h"
+#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/utils.h>
+#include <pappsomspp/grouping/grpprotein.h>
+
+MassChroQml::MassChroQml(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 MassChroqML output file : %1\n").arg(out_filename));
+ }
+
+ _output_stream->setAutoFormatting(true);
+ _output_stream->writeStartDocument("1.0");
+
+
+}
+
+MassChroQml::~MassChroQml()
+{
+ delete _output_file;
+ delete _output_stream;
+}
+
+void MassChroQml::close() {
+ _output_stream->writeEndDocument();
+ _output_file->close();
+}
+
+void MassChroQml::write(ProjectSp sp_project) {
+
+ _sp_project = sp_project;
+ if (_sp_project.get() == nullptr) {
+ throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n project is empty"));
+ }
+
+ //<masschroq>
+ _output_stream->writeStartElement("masschroq");
+ _output_stream->writeAttribute("type","input");
+ _output_stream->writeAttribute("version","2.2");
+ //_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/masschroqml/2.2");
+ //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/masschroqml/2.2 http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+
+ // <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();
+}
+void MassChroQml::writePeptideList() {
+//<peptide_list>
+ _output_stream->writeStartElement("peptide_list");
+ /*
+ <peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
+ seq="TCVADESHAGCEK">
+ <modifications><!-- this tag is optional but gives an exact mass computation -->
+ <psimod at="2" acc="MOD:00397"></psimod>
+ <psimod at="11" acc="MOD:00397"></psimod>
+ </modifications>
+ <observed_in data="samp0" scan="655" z="2" />
+ <observed_in data="samp1" scan="798" z="2" />
+ </peptide>
+ <peptide id="pep1" mh="1103.461" mods="57.04" prot_ids="P1.1"
+ seq="ADESHAGCEK">
+ <modifications><!-- this tag is optional but gives an exact mass computation -->
+ <psimod at="8" acc="MOD:00397"></psimod>
+ </modifications>
+ <observed_in data="samp3" scan="663" z="2" />
+ </peptide>*/
+ //</peptide_list>
+ _output_stream->writeEndElement();
+}
+
+void MassChroQml::writeGroups() {
+//<groups>
+ _output_stream->writeStartElement("groups");
+ //<group data_ids="samp0 samp1" id="G1" />
+ _output_stream->writeStartElement("group");
+ _output_stream->writeAttribute("id",QString("fractiona1"));
+ std::vector<MsRunSp> msrun_list = _sp_project.get()->getMsRunStore().getMsRunList();
+ QStringList list;
+ for (MsRunSp & msrun : msrun_list) {
+ list << msrun.get()->getXmlId();
+ }
+ _output_stream->writeAttribute("data_ids",list.join(" "));
+ _output_stream->writeEndElement();
+ //<group data_ids="samp2 samp3" id="G2" />
+// </groups>
+ _output_stream->writeEndElement();
+}
+
+void MassChroQml::writeProteinList() {
+//<protein_list>
+ _output_stream->writeStartElement("protein_list");
+ std::vector<IdentificationGroup *> identification_list = _sp_project.get()->getIdentificationGroupList();
+ if (identification_list.size() == 0) {
+ throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n no protein list"));
+ }
+ if (identification_list.size() > 1) {
+ throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n only available in combine mode"));
+ }
+ _p_identification_group = identification_list[0];
+ for (ProteinMatch * p_protein_match :_p_identification_group->getProteinMatchList()) {
+ if (!p_protein_match->isGrouped()) continue;
+ //<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
+ // id="P1.1" />
+ pappso::GrpProteinSp grp_protein = p_protein_match->getGrpProteinSp();
+ if (grp_protein.get()->getRank() == 1) {
+ _output_stream->writeStartElement("protein");
+ _output_stream->writeAttribute("id",grp_protein.get()->getGroupingId());
+ QStringList list;
+ list << p_protein_match->getProteinXtpSp().get()->getAccession();
+ list << p_protein_match->getProteinXtpSp().get()->getDescription();
+ _output_stream->writeAttribute("desc",list.join(" "));
+ //<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR."
+ // id="P1.2" />
+ _output_stream->writeEndElement();
+ }
+ }
+ //</protein_list>
+ _output_stream->writeEndElement();
+}
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
new file mode 100644
index 0000000000000000000000000000000000000000..47559be08346f242c118f6b399bd9742599a297b
--- /dev/null
+++ b/src/output/masschroqml.h
@@ -0,0 +1,57 @@
+/**
+ * \file output/masschroqml.h
+ * \date 7/4/2017
+ * \author Olivier Langella
+ * \brief MassChroQML 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 MASSCHROQML_H
+#define MASSCHROQML_H
+
+#include <QXmlStreamWriter>
+#include <QFile>
+#include <QString>
+#include "../core/project.h"
+
+class MassChroQml
+{
+ public:
+ MassChroQml(const QString & out_filename);
+ ~MassChroQml();
+
+ void write(ProjectSp sp_project);
+ void close();
+private:
+ void writeGroups();
+ void writeProteinList();
+ void writePeptideList();
+private :
+ QFile * _output_file;
+ QXmlStreamWriter * _output_stream;
+ ProjectSp _sp_project;
+ IdentificationGroup * _p_identification_group;
+};
+
+#endif // MASSCHROQML_H
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index 1fee9ca9e8418400fe66135d1d8e8a0e353729f5..ee6c13061885896b559066d3e86a9f1f70321062 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -30,6 +30,7 @@
#include "msrunstore.h"
#include <pappsomspp/exception/exceptionnotfound.h>
+#include <pappsomspp/utils.h>
MsRunStore::MsRunStore()
{
@@ -49,9 +50,19 @@ MsRunSp MsRunStore::getInstance(const QString & location) {
}
else {
MsRunSp p_xtfile = std::make_shared<MsRun>(location);
+ p_xtfile.get()->setXmlId(QString("samp%1").arg(pappso::Utils::getLexicalOrderedString(_map_msrun.size())));
_map_msrun.insert(std::pair< QString, MsRunSp >(location, p_xtfile));
return p_xtfile;
}
throw pappso::ExceptionNotFound(QObject::tr("Ms resource %1 not found").arg(location));
}
+
+
+std::vector<MsRunSp> MsRunStore::getMsRunList() const {
+ std::vector<MsRunSp> msrun_list;
+ for (auto & msrun_pair :_map_msrun) {
+ msrun_list.push_back(msrun_pair.second);
+ }
+ return msrun_list;
+}
diff --git a/src/utils/msrunstore.h b/src/utils/msrunstore.h
index 27e6df6f26cc0bd37c3d5ecee7b294223af9f036..0741d45a7777a547b31f1de3683870b4247aa3c1 100644
--- a/src/utils/msrunstore.h
+++ b/src/utils/msrunstore.h
@@ -33,6 +33,7 @@
#include <QString>
#include <map>
+#include <vector>
#include "../core/msrun.h"
class MsRunStore
@@ -42,6 +43,8 @@ public:
~MsRunStore();
MsRunSp getInstance(const QString & location);
+
+ std::vector<MsRunSp> getMsRunList() const;
private:
std::map<QString, MsRunSp> _map_msrun;
};
diff --git a/src/utils/types.h b/src/utils/types.h
index 3bf0931e26f444e13db4fe087d87c5e9ae4face8..7a5be71be3a1735e6984713699b0ef4356a741de 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -37,6 +37,15 @@ enum class GroupingType {
};
+/** \def MzFormat mz data file format types
+ *
+ */
+
+enum class MzFormat {
+ mzML, ///< mzML
+ mzXML, ///< mzXML
+};
+
/** \def ProteinListColumn list of available fields to display in protein list
*
*/