From 9fe2407e01a39e735eca10cf083ee8f11716cf37 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 22 Mar 2017 12:06:46 +0100
Subject: [PATCH] first working grouping algo
---
src/CMakeLists.txt | 1 +
src/core/identificationgroup.cpp | 12 +
src/core/identificationgroup.h | 3 +
src/core/project.cpp | 8 +
src/core/project.h | 4 +
src/core/proteinmatch.cpp | 23 ++
src/core/proteinmatch.h | 19 +-
src/grouping/groupingexperiment.cpp | 11 +
src/grouping/groupingexperiment.h | 15 +-
src/grouping/groupingpeptidemass.cpp | 52 ++++
src/grouping/groupingpeptidemass.h | 47 +++
src/gui/mainwindow.cpp | 16 +-
.../protein_list_view/proteinlistwindow.cpp | 3 +-
src/gui/protein_list_view/proteinlistwindow.h | 2 +-
.../protein_list_view/proteintablemodel.cpp | 48 ++--
src/gui/protein_list_view/proteintablemodel.h | 2 +
src/resources/xtandempipeline_icon.svg | 270 +++++++++++++-----
src/utils/types.h | 39 +++
18 files changed, 465 insertions(+), 110 deletions(-)
create mode 100644 src/grouping/groupingpeptidemass.cpp
create mode 100644 src/grouping/groupingpeptidemass.h
create mode 100644 src/utils/types.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 5385f2566..6bc8c3534 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -64,6 +64,7 @@ SET(CPP_FILES
core/identification_sources/identificationxtandemfile.cpp
files/xpipfile.cpp
grouping/groupingexperiment.cpp
+ grouping/groupingpeptidemass.cpp
input/xpipsaxhandler.cpp
utils/peptidestore.cpp
utils/readspectrum.cpp
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 7b86a9081..a6ac7bec6 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -77,3 +77,15 @@ size_t IdentificationGroup::countValid()const {
}
return i;
}
+
+void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
+ if (_p_grp_experiment != nullptr) {
+ delete _p_grp_experiment;
+ }
+ _p_grp_experiment = GroupingExperiment::newInstance(grouping_type);
+ for (auto & p_protein_match : _protein_match_list) {
+ p_protein_match->setGroupingExperiment(_p_grp_experiment);
+ }
+
+ _p_grp_experiment->startGrouping();
+}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 75337244b..961d0f71b 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -26,6 +26,7 @@
#include <pappsomspp/msrun/msrunid.h>
#include "grouping/groupingexperiment.h"
+#include "../utils/types.h"
#ifndef IDENTIFICATIONGROUP_H
#define IDENTIFICATIONGROUP_H
@@ -54,6 +55,8 @@ public:
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+
+ void startGrouping (const GroupingType & grouping_type);
private :
GroupingExperiment * _p_grp_experiment= nullptr;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 3e6a0955d..f4a69901d 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -88,3 +88,11 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
return _p_current_identification_group;
}
+
+
+void Project::startGrouping() {
+ for (auto & p_id_group : _identification_goup_list) {
+ p_id_group->startGrouping(_grouping_type);
+ }
+
+}
diff --git a/src/core/project.h b/src/core/project.h
index b5ddcdf6a..5992dbf88 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -26,6 +26,7 @@
#include<memory>
#include "identificationgroup.h"
#include "automaticfilterparameters.h"
+#include "utils/types.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -47,6 +48,7 @@ public:
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+ void startGrouping();
private :
@@ -54,6 +56,8 @@ private :
IdentificationGroup* _p_current_identification_group = nullptr;
AutomaticFilterParameters _automatic_filter_parameters;
+
+ GroupingType _grouping_type = GroupingType::PeptideMass;
};
#endif // PROJECT_H
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 05432afa2..31181bb78 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -23,6 +23,7 @@
#include "proteinmatch.h"
#include <pappsomspp/msrun/msrunid.h>
+#include <pappsomspp/grouping/grpprotein.h>
ProteinMatch::ProteinMatch()
@@ -110,3 +111,25 @@ void ProteinMatch::addPeptideMatch(PeptideMatch * peptide_match) {
std::vector<PeptideMatch *> & ProteinMatch::getPeptideMatchList() {
return _peptide_match_list;
}
+
+void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment) {
+ if (isValidAndChecked()) {
+ _sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
+
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->isValidAndChecked()) {
+ p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match);
+ }
+ }
+ }
+}
+
+QString ProteinMatch::getStringGroupSubgroupNumber() const {
+ if (_sp_grp_protein.get() != nullptr) {
+ if (_sp_grp_protein.get()->getGroupNumber() > 0) {
+ return _sp_grp_protein.get()->getGroupingId();
+ }
+ }
+ QString number;
+ return number;
+}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 298355014..d6500acf6 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -26,6 +26,7 @@
#include "proteinxtp.h"
#include "peptidematch.h"
#include "automaticfilterparameters.h"
+#include "../grouping/groupingexperiment.h"
#ifndef PROTEINMATCH_H
#define PROTEINMATCH_H
@@ -35,7 +36,7 @@ class ProteinMatch
public:
ProteinMatch();
~ProteinMatch();
-
+
const ProteinXtpSp & getProteinXtpSp() const;
void setEvalue(pappso::pappso_double evalue);
pappso::pappso_double getEvalue() const;
@@ -43,23 +44,29 @@ public:
void addPeptideMatch(PeptideMatch * peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
void setChecked(bool arg1);
-
+
bool isChecked() const;
bool isValid() const;
bool isValidAndChecked() const;
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
+
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+ void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
+
+ QString getStringGroupSubgroupNumber() const;
+
private:
+ pappso::GrpProteinSp _sp_grp_protein;
+
std::vector<PeptideMatch *> _peptide_match_list;
ProteinXtpSp _protein_sp = nullptr;
pappso::pappso_double _evalue=0;
/** @brief manually checked by user (true by default)
*/
bool _checked = true;
-
+
/** @brief automatic filter result (false by default)
*/
bool _proxy_valid = false;
diff --git a/src/grouping/groupingexperiment.cpp b/src/grouping/groupingexperiment.cpp
index 717e7580f..8183207f7 100644
--- a/src/grouping/groupingexperiment.cpp
+++ b/src/grouping/groupingexperiment.cpp
@@ -22,6 +22,8 @@
******************************************************************************/
#include "groupingexperiment.h"
+#include <pappsomspp/exception/exceptionnotimplemented.h>
+#include "groupingpeptidemass.h"
GroupingExperiment::GroupingExperiment()
{
@@ -32,3 +34,12 @@ GroupingExperiment::~GroupingExperiment()
{
}
+
+GroupingExperiment * GroupingExperiment::newInstance(const GroupingType & grouping_type) {
+ if (grouping_type == GroupingType::PeptideMass) {
+ return new GroupingPeptideMass();
+ }
+ else {
+ throw pappso::ExceptionNotImplemented(QObject::tr("Grouping algorithm not yet implemented"));
+ }
+}
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
index f473f2c6b..2c4353966 100644
--- a/src/grouping/groupingexperiment.h
+++ b/src/grouping/groupingexperiment.h
@@ -22,16 +22,27 @@
******************************************************************************/
+#include "../utils/types.h"
+#include <pappsomspp/grouping/grpexperiment.h>
+
#ifndef GROUPINGEXPERIMENT_H
#define GROUPINGEXPERIMENT_H
+class ProteinMatch;
+class PeptideMatch;
+
class GroupingExperiment
{
public:
GroupingExperiment();
~GroupingExperiment();
-
-
+
+ static GroupingExperiment * newInstance(const GroupingType & grouping_type);
+
+ virtual pappso::GrpProteinSp getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
+ virtual void setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) = 0;
+ virtual void startGrouping()= 0;
+
};
#endif // GROUPINGEXPERIMENT_H
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
new file mode 100644
index 000000000..b88da4769
--- /dev/null
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -0,0 +1,52 @@
+
+/*******************************************************************************
+* 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 "groupingpeptidemass.h"
+#include "../core/proteinmatch.h"
+#include "../core/peptidematch.h"
+
+GroupingPeptideMass::GroupingPeptideMass()
+{
+
+ _p_monitor = new pappso::GrpGroupingMonitor();
+ _p_grp_experiment = new pappso::GrpExperiment(*_p_monitor);
+
+}
+
+GroupingPeptideMass::~GroupingPeptideMass()
+{
+ delete _p_grp_experiment;
+ delete _p_monitor;
+}
+
+pappso::GrpProteinSp GroupingPeptideMass::getGrpProteinSp(ProteinMatch* p_protein_match) {
+ return _p_grp_experiment->getGrpProteinSp(p_protein_match->getProteinXtpSp().get()->getAccession(),p_protein_match->getProteinXtpSp().get()->getDescription());
+}
+void GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) {
+
+ _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_match->getPeptideSp().get()->getSequence(), p_peptide_match->getPeptideSp().get()->getMass());
+}
+
+void GroupingPeptideMass::startGrouping() {
+ _p_grp_experiment->startGrouping();
+}
diff --git a/src/grouping/groupingpeptidemass.h b/src/grouping/groupingpeptidemass.h
new file mode 100644
index 000000000..0738445ac
--- /dev/null
+++ b/src/grouping/groupingpeptidemass.h
@@ -0,0 +1,47 @@
+
+/*******************************************************************************
+* 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 "groupingexperiment.h"
+
+#ifndef GROUPINGPEPTIDEMASS_H
+#define GROUPINGPEPTIDEMASS_H
+
+class GroupingPeptideMass: public GroupingExperiment
+{
+ friend class GroupingExperiment;
+public:
+
+ virtual ~GroupingPeptideMass();
+
+ virtual pappso::GrpProteinSp getGrpProteinSp(ProteinMatch* p_protein_match) override;
+ virtual void setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
+ virtual void startGrouping() override;
+
+protected :
+ GroupingPeptideMass();
+
+private :
+ pappso::GrpGroupingMonitor * _p_monitor;
+ pappso::GrpExperiment * _p_grp_experiment;
+};
+
+#endif // GROUPINGPEPTIDEMASS_H
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 139afaeb1..cf31011b2 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -50,11 +50,11 @@ MainWindow::MainWindow(QWidget *parent):
*/
workerThread.start();
- QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
+ //QDockWidget *dock = new QDockWidget(tr("Protein List"), this);
_protein_list_window = new ProteinListWindow(this);
- //_protein_list_window->show();
- dock->setWidget(_protein_list_window);
- addDockWidget(Qt::RightDockWidgetArea, dock);
+ _protein_list_window->show();
+ //dock->setWidget(_protein_list_window);
+ //addDockWidget(Qt::RightDockWidgetArea, dock);
#if QT_VERSION >= 0x050000
@@ -128,7 +128,13 @@ void MainWindow::selectXpipFile() {
_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
}
catch (pappso::PappsoException & error) {
- viewError(error.qwhat());
+ viewError(tr("Error while reading XPIP file :\n%1").arg(error.qwhat()));
+ }
+ try {
+ _project_sp.get()->startGrouping();
+ }
+ catch (pappso::PappsoException & error) {
+ viewError(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 60248bf10..bf1e2492b 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -57,13 +57,14 @@ ProteinListWindow::ProteinListWindow(MainWindow *parent):
#else
// Qt4 code
connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
+ connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
connect(ui->proteinSearchEdit, SIGNAL(textChanged(QString)), _protein_table_model_p, SLOT(onProteinSearchEdit(QString)));
//connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
#endif
}
-void ProteinListWindow::clickOnproteinMatch(ProteinMatch * p_protein_match) {
+void ProteinListWindow::doubleclickOnproteinMatch(ProteinMatch * p_protein_match) {
emit proteinMatchClicked(p_protein_match);
//updateStatusBar();
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index dea9dd09c..b4c960dec 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -43,7 +43,7 @@ public:
explicit ProteinListWindow(MainWindow * parent = 0);
~ProteinListWindow();
void setIdentificationGroup(IdentificationGroup * p_identification_group);
- void clickOnproteinMatch(ProteinMatch * p_protein_match);
+ void doubleclickOnproteinMatch(ProteinMatch * p_protein_match);
void updateStatusBar();
public slots:
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 17c8a1c96..16745f411 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -45,6 +45,12 @@ void ProteinTableProxyModel::onTableClicked(const QModelIndex &index)
_protein_table_model_p->onTableClicked(this->mapToSource(index));
}
+void ProteinTableProxyModel::onTableDoubleClicked(const QModelIndex &index)
+{
+ qDebug() << "ProteinTableProxyModel::onTableDoubleClicked begin " << index.row();
+ qDebug() << "ProteinTableProxyModel::onTableDoubleClicked begin " << this->mapToSource(index).row();
+ _protein_table_model_p->onTableDoubleClicked(this->mapToSource(index));
+}
bool ProteinTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
QVariant leftData = sourceModel()->data(left);
QVariant rightData = sourceModel()->data(right);
@@ -132,10 +138,12 @@ QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation,
case 0:
return QString("checked");
case 1:
- return QString("accession");
+ return QString("group");
case 2:
- return QString("protein description");
+ return QString("accession");
case 3:
+ return QString("protein description");
+ case 4:
return QString("Evalue");
}
}
@@ -163,31 +171,32 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
}
break;
case Qt::DisplayRole:
+ if (_p_identification_group == nullptr) {
+ return QVariant();
+ }
if (col == 0) {
return QVariant();
}
+
if (col == 1) {
- if (_p_identification_group != nullptr) {
- return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession();
- }
+ return _p_identification_group->getProteinMatchList().at(row)->getStringGroupSubgroupNumber();
}
+
if (col == 2) {
- if (_p_identification_group != nullptr) {
- return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
- }
+ return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession();
+
}
if (col == 3) {
- if (_p_identification_group != nullptr) {
+ return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
- return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
- }
}
-
if (col == 4) {
- if (_p_identification_group != nullptr) {
+ return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
- return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
- }
+ }
+
+ if (col == 5) {
+ return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
}
return QString("Row%1, Column%2")
@@ -212,10 +221,13 @@ void ProteinTableModel::onTableClicked(const QModelIndex &index)
//emit dataChanged(index, index);
_p_protein_list_window->updateStatusBar();
}
+}
- else {
- _p_protein_list_window->clickOnproteinMatch(_p_identification_group->getProteinMatchList().at(row));
- }
+void ProteinTableModel::onTableDoubleClicked(const QModelIndex &index)
+{
+ int row = index.row();
+ int col = index.column();
+ _p_protein_list_window->doubleclickOnproteinMatch(_p_identification_group->getProteinMatchList().at(row));
}
bool ProteinTableModel::acceptRow(int source_row) {
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index 715be5986..53f642e95 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -44,6 +44,7 @@ public:
public slots:
void onTableClicked(const QModelIndex &index);
+ void onTableDoubleClicked(const QModelIndex &index);
private:
double m_minGravity;
double m_minDensity;
@@ -66,6 +67,7 @@ public:
public slots:
void onTableClicked(const QModelIndex &index);
+ void onTableDoubleClicked(const QModelIndex &index);
void onProteinSearchEdit(QString protein_search_string);
private :
IdentificationGroup * _p_identification_group = nullptr;
diff --git a/src/resources/xtandempipeline_icon.svg b/src/resources/xtandempipeline_icon.svg
index 0ba818fef..32c7eef0f 100644
--- a/src/resources/xtandempipeline_icon.svg
+++ b/src/resources/xtandempipeline_icon.svg
@@ -7,19 +7,32 @@
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
width="60"
height="60"
id="svg2"
version="1.1"
- inkscape:version="0.48.0 r9654"
- sodipodi:docname="logo.svg"
+ inkscape:version="0.48.5 r10040"
+ sodipodi:docname="xtandempipeline_icon.svg"
inkscape:export-filename="/home/valot/developpement/eclipse_java/MSMS_Xtandem/src/resources/images/icon_64.png"
inkscape:export-xdpi="96"
inkscape:export-ydpi="96">
<defs
id="defs4">
+ <linearGradient
+ inkscape:collect="always"
+ id="linearGradient3810">
+ <stop
+ style="stop-color:#000000;stop-opacity:1;"
+ offset="0"
+ id="stop3812" />
+ <stop
+ style="stop-color:#000000;stop-opacity:0;"
+ offset="1"
+ id="stop3814" />
+ </linearGradient>
<filter
color-interpolation-filters="sRGB"
inkscape:collect="always"
@@ -38,6 +51,123 @@
stdDeviation="0.70158516"
id="feGaussianBlur3951-6" />
</filter>
+ <linearGradient
+ inkscape:collect="always"
+ xlink:href="#linearGradient3810"
+ id="linearGradient3816"
+ x1="474.67546"
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+ gradientUnits="userSpaceOnUse"
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+ <linearGradient
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+ gradientUnits="userSpaceOnUse"
+ x1="474.67546"
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+ <linearGradient
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diff --git a/src/utils/types.h b/src/utils/types.h
new file mode 100644
index 000000000..bc7c3b7f7
--- /dev/null
+++ b/src/utils/types.h
@@ -0,0 +1,39 @@
+
+/*******************************************************************************
+* 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 _TYPES_H_
+#define _TYPES_H_ 1
+
+/*********** enumerations *********************************/
+
+/** \def GroupingType list of available grouping algoritms
+ *
+ */
+enum class GroupingType {
+ PeptideMass, ///< protein grouper algo
+ Phospho, ///< phospho peptides grouping
+ SampleScan ///< X!TandemPipeline algo
+};
+
+#endif /* _TYPES_H_ */
--
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