diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6bc8c3534f2d9ad1261fab6a9846a492f03e0e5b..e7f5f5a40729d02caab735060f09a47e729cacd9 100644
--- a/src/CMakeLists.txt
+++ b/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} )
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 718d2e02591040041d1af213b7871797f1956a15..03d83fd1a513e009791fa4abc64d204fb9a9ef75 100644
--- a/src/core/peptidematch.cpp
+++ b/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
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 8d8f2664116bbb55f8d06be217ee6c0e14334531..0a03107a14bb537364b9ce865931b0155305f8b7 100644
--- a/src/core/peptidematch.h
+++ b/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;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 31181bb787ee71a0bd2993ababb68fcedad02cfe..f8b124f2caecca2238ecfffdb25aff69181623c0 100644
--- a/src/core/proteinmatch.cpp
+++ b/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));
}
}
}
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
index 2c4353966be4b6a51c2c92ad5f54975ec5ebd813..e05d9e0f1aefc44c7916f2347be4ea7de98a1d3c 100644
--- a/src/grouping/groupingexperiment.h
+++ b/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;
};
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index b88da4769321b270bfb8869c2f4095e190abedae..c5d6c430d6f34b0fe4fcb141f6d02939fcb8cc7c 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/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() {
diff --git a/src/grouping/groupingpeptidemass.h b/src/grouping/groupingpeptidemass.h
index 0738445ac36e488c22637977f6af61fa01c0f47e..f6644b57d54749ccb4c99c90388bbffbd3a85e3a 100644
--- a/src/grouping/groupingpeptidemass.h
+++ b/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 :
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index f5e88e48c77b5d10e465053453f3ff3042c28b06..9fe229a9b18ea7daeea01e1d22bf0226d1007e59 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/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();
}
}
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 16745f411eca3384ad8f8baa3714f5c8755b9029..25b28d48e3e4574f587474e45bd30c28ae63008a 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/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
{