first working grouping algo

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

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();
+}

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;
 

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);
+    }
+
+}

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

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;
+}

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;

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"));
+    }
+}

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

src/grouping/groupingpeptidemass.cpp

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

src/grouping/groupingpeptidemass.h

+
+/*******************************************************************************
+* 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

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()));
     }
 
 }

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();
 }

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:

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) {

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;

src/resources/xtandempipeline_icon.svg

@@ -7,19 +7,32 @@
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    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"
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    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">
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+       inkscape:collect="always"
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+         offset="0"
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+      <stop
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+         offset="1"
+         id="stop3814" />
+    </linearGradient>
     <filter
        color-interpolation-filters="sRGB"
        inkscape:collect="always"
@@ -38,6 +51,123 @@
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@@ -58,8 +188,8 @@
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-     inkscape:window-x="1280"
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@@ -69,7 +199,7 @@
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-        <dc:title></dc:title>
+        <dc:title />
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@@ -78,89 +208,75 @@
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src/utils/types.h

+
+/*******************************************************************************
+* 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_ */