new grouping API

src/CMakeLists.txt

@@ -28,11 +28,11 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 
 #sudo apt-get install libpappsomspp-dev
-FIND_PACKAGE( Pappsomspp REQUIRED )
+#FIND_PACKAGE( Pappsomspp REQUIRED )
 #SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
- #SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
- #SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/build/src/libpappsomspp-qt4.so")
+ SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
 
 INCLUDE_DIRECTORIES( ${PAPPSOMSPP_INCLUDE_DIR} )
 

src/core/peptidematch.cpp

@@ -32,7 +32,7 @@ void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
     _proxy_valid = false;
 
     if (_evalue <= automatic_filter_parameters.getFilterPeptideEvalue()) {
-      _proxy_valid = true;
+        _proxy_valid = true;
     }
 }
 void PeptideMatch::setRetentionTime(pappso::pappso_double rt) {
@@ -70,7 +70,7 @@ bool PeptideMatch::isChecked() const {
     return _checked;
 }
 
-bool PeptideMatch::isValidAndChecked() const{
+bool PeptideMatch::isValidAndChecked() const {
     return _proxy_valid && _checked;
 }
 void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
@@ -89,10 +89,17 @@ unsigned int PeptideMatch::getCharge() const {
     return _charge;
 }
 
-pappso::PeptideSp PeptideMatch::getPeptideSp() const {
+const pappso::PeptideSp & PeptideMatch::getPeptideSp() const {
     return _peptide_sp;
 }
 
 const pappso::MsRunIdSp & PeptideMatch::getMsRunIdSp() const {
-  return _msrunid_sp;
-}
\ No newline at end of file
+    return _msrunid_sp;
+}
+void PeptideMatch::setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide) {
+    _sp_grp_peptide =sp_grp_peptide;
+}
+
+    const pappso::GrpPeptideSp & PeptideMatch::getGrpPeptideSp() const {
+      return _sp_grp_peptide;
+    }
\ No newline at end of file

src/core/peptidematch.h

@@ -29,6 +29,8 @@
 #include "identification_sources/identificationdatasource.h"
 #include "automaticfilterparameters.h"
 
+#include "../grouping/groupingexperiment.h"
+
 class PeptideMatch
 {
 public :
@@ -51,8 +53,11 @@ public :
     unsigned int getScan() const;
     pappso::pappso_double getRetentionTime() const;
     unsigned int getCharge() const;
-    pappso::PeptideSp getPeptideSp() const;
+    const pappso::PeptideSp & getPeptideSp() const;
     pappso::pappso_double getEvalue() const;
+    
+    void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
+    const pappso::GrpPeptideSp & getGrpPeptideSp() const;
 
            /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
      * */
@@ -61,6 +66,7 @@ public :
 private :
     pappso::MsRunIdSp _msrunid_sp;
     unsigned int _scan;
+    pappso::GrpPeptideSp _sp_grp_peptide;
     pappso::PeptideSp _peptide_sp;
     pappso::pappso_double _rt;
     pappso::pappso_double _evalue;

src/core/proteinmatch.cpp

@@ -118,7 +118,7 @@ void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment)
 
         for (auto & p_peptide_match : _peptide_match_list) {
            if (p_peptide_match->isValidAndChecked()) {
-	     p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match);
+	     p_peptide_match->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match));
 	   }
         }
     }

src/grouping/groupingexperiment.h

@@ -39,8 +39,8 @@ public:
 
     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 pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
+    virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) = 0;
     virtual void startGrouping()= 0;
 
 };

src/grouping/groupingpeptidemass.cpp

@@ -29,7 +29,7 @@ GroupingPeptideMass::GroupingPeptideMass()
 {
 
     _p_monitor = new pappso::GrpGroupingMonitor();
-    _p_grp_experiment = new pappso::GrpExperiment(*_p_monitor);
+    _p_grp_experiment = new pappso::GrpExperiment(_p_monitor);
 
 }
 
@@ -39,12 +39,12 @@ GroupingPeptideMass::~GroupingPeptideMass()
     delete _p_monitor;
 }
 
-pappso::GrpProteinSp GroupingPeptideMass::getGrpProteinSp(ProteinMatch* p_protein_match) {
+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) {
+pappso::GrpPeptideSp & 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());
+    return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_match->getPeptideSp().get()->getSequence(), p_peptide_match->getPeptideSp().get()->getMass());
 }
 
 void GroupingPeptideMass::startGrouping() {

src/grouping/groupingpeptidemass.h

@@ -32,8 +32,8 @@ public:
 
     virtual ~GroupingPeptideMass();
 
-    virtual pappso::GrpProteinSp getGrpProteinSp(ProteinMatch* p_protein_match) override;
-    virtual void setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
+    virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) override;
+    virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
     virtual void startGrouping() override;
 
 protected :

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -95,7 +95,7 @@ int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
     return 0;
 }
 int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
-    return 6;
+    return 7;
 }
 QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
 {
@@ -107,14 +107,16 @@ QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation,
             case 0:
                 return QString("checked");
             case 1:
-                return QString("sample");
+                return QString("peptide ID");
             case 2:
-                return QString("scan");
+                return QString("sample");
             case 3:
-                return QString("RT");
+                return QString("scan");
             case 4:
-                return QString("charge");
+                return QString("RT");
             case 5:
+                return QString("charge");
+            case 6:
                 return QString("sequence");
             }
         }
@@ -152,15 +154,18 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
                 return _p_protein_match->getPeptideMatchList().at(row)->getIdentificationDataSource()->getResourceName();
             }
             if (col == 2) {
-                return QVariant ((quint16) _p_protein_match->getPeptideMatchList().at(row)->getScan());
+                return _p_protein_match->getPeptideMatchList().at(row)->getIdentificationDataSource()->getResourceName();
             }
             if (col == 3) {
-                return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
+                return QVariant ((quint16) _p_protein_match->getPeptideMatchList().at(row)->getScan());
             }
             if (col == 4) {
-                return QVariant ((quint8) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
+                return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
             }
             if (col == 5) {
+                return QVariant ((quint8) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
+            }
+            if (col ==6) {
                 return _p_protein_match->getPeptideMatchList().at(row)->getPeptideSp().get()->getSequence();
             }
         }

src/gui/protein_list_view/proteintablemodel.cpp

@@ -126,7 +126,7 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
     return 0;
 }
 int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
-    return 4;
+    return 5;
 }
 QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
 {