protein store and peptide store inside the project, contaminant groups removed

src/CMakeLists.txt

@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 #sudo apt-get install libpappsomspp-dev
 #FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+ 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}/cbuild/src/libpappsomspp-qt4.so")
 

src/core/project.cpp

@@ -39,6 +39,14 @@ Project::~Project()
     }
 }
 
+PeptideStore & Project::getPeptideStore() {
+    return _peptide_store;
+}
+
+ProteinStore & Project::getProteinStore() {
+    return _protein_store;
+}
+
 void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
     _automatic_filter_parameters = automatic_filter_parameters;
     for (auto & p_id_group : _identification_goup_list) {
@@ -91,7 +99,7 @@ IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
 
 
 void Project::startGrouping() {
-      for (auto & p_id_group : _identification_goup_list) {
+    for (auto & p_id_group : _identification_goup_list) {
         p_id_group->startGrouping(_grouping_type);
     }
 

src/core/project.h

@@ -26,7 +26,9 @@
 #include<memory>
 #include "identificationgroup.h"
 #include "automaticfilterparameters.h"
-#include "utils/types.h"
+#include "../utils/types.h"
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
 
 class Project;
 typedef std::shared_ptr<Project> ProjectSp;
@@ -41,6 +43,8 @@ public:
     ~Project();
 
     ProjectSp makeProjectSp() const;
+    ProteinStore & getProteinStore();
+    PeptideStore & getPeptideStore();
     void readXpipFile(QFileInfo xpip_source);
     IdentificationGroup* newIdentificationGroup();
     IdentificationGroup* getCurrentIdentificationGroupP() const;
@@ -58,6 +62,9 @@ private :
     AutomaticFilterParameters _automatic_filter_parameters;
     
     GroupingType _grouping_type = GroupingType::PeptideMass;
+    
+    ProteinStore _protein_store;
+    PeptideStore _peptide_store;
 };
 
 #endif // PROJECT_H

src/core/proteinmatch.cpp

@@ -116,13 +116,19 @@ void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment)
     _sp_grp_protein = nullptr;
     if (isValidAndChecked()) {
         _sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
-
+ 
         for (auto & p_peptide_match : _peptide_match_list) {
             p_peptide_match->setGrpPeptideSp(nullptr);
             if (p_peptide_match->isValidAndChecked()) {
                 p_peptide_match->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match));
             }
         }
+        
+               
+        if (_protein_sp.get()->isContaminant()) {
+            p_grp_experiment->addPostGroupingGrpProteinSpRemoval(_sp_grp_protein);
+        }
+
     }
 }
 

src/core/proteinxtp.cpp

@@ -55,9 +55,9 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
     void ProteinXtp::setIsDecoy(bool conta){
         _is_decoy = conta;
     }
-    bool ProteinXtp::getIsContaminant() const{
+    bool ProteinXtp::isContaminant() const{
         return _is_contaminant;
     }
-    bool ProteinXtp::getIsDecoy() const{
+    bool ProteinXtp::isDecoy() const{
         return _is_decoy;
     }

src/core/proteinxtp.h

@@ -46,8 +46,8 @@ public:
     
     void setIsContaminant(bool conta);
     void setIsDecoy(bool conta);
-    bool getIsContaminant() const;
-    bool getIsDecoy() const;
+    bool isContaminant() const;
+    bool isDecoy() const;
 
 private:
     SequenceDatabase * _p_sequence_database;

src/grouping/groupingexperiment.h

@@ -41,6 +41,7 @@ public:
 
     virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
     virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) = 0;
+    virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) = 0;
     virtual void startGrouping()= 0;
 
 };

src/grouping/groupingpeptidemass.cpp

@@ -50,3 +50,7 @@ pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp p
 void GroupingPeptideMass::startGrouping() {
     _p_grp_experiment->startGrouping();
 }
+
+void GroupingPeptideMass::addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) {
+    _p_grp_experiment->addPostGroupingGrpProteinSpRemoval(sp_protein);
+}

src/grouping/groupingpeptidemass.h

@@ -34,6 +34,8 @@ public:
 
     virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) override;
     virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
+    virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) override;
+
     virtual void startGrouping() override;
 
 protected :

src/input/xpipsaxhandler.cpp

@@ -24,6 +24,8 @@
 #include <pappsomspp/msrun/msrunid.h>
 #include <pappsomspp/exception/exceptionnotfound.h>
 #include <cmath>
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
 
 XpipSaxHandler::XpipSaxHandler(Project * p_project):_p_project(p_project)
 {
@@ -277,7 +279,7 @@ bool XpipSaxHandler::endElement_peptide() {
     qDebug() << "endElement_peptide ";
 
     pappso::PeptideSp peptide_const = pappso::Peptide(*(_current_peptide_sp.get())).makePeptideSp();
-    peptide_const = _peptide_store.getInstance(peptide_const);
+    peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
     _p_peptide_match->setPeptideSp(peptide_const);
     return true;
 }
@@ -292,7 +294,9 @@ bool XpipSaxHandler::endElement_sequence() {
     return true;
 }
 bool XpipSaxHandler::endElement_protein() {
-    _p_protein_match->setProteinXtpSp(_current_protein.makeProteinXtpSp());
+    ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
+    
+    _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
 
     return true;
 }

src/input/xpipsaxhandler.h

@@ -30,7 +30,6 @@
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "../core/project.h"
 #include "../core/proteinmatch.h"
-#include "../utils/peptidestore.h"
 
 class XpipSaxHandler: public QXmlDefaultHandler
 {
@@ -87,7 +86,6 @@ private:
     pappso::NoConstPeptideSp _current_peptide_sp;
     IdentificationGroup * _current_identification_group_p;
     
-    PeptideStore _peptide_store;
     QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
     QMap<QString, pappso::MsRunIdSp> _map_msrunid;
 };

src/utils/proteinstore.cpp

@@ -28,13 +28,14 @@
 ******************************************************************************/
 
 #include "proteinstore.h"
+#include <QDebug>
 
 
 ProteinStore::ProteinStore()
 {
-_regexp_contaminant.setPattern("([KR])([^P])");
+    _regexp_contaminant.setPattern("^conta\\|");
 
-_regexp_decoy.setPattern(".*\\|reversed$");
+    _regexp_decoy.setPattern(".*\\|reversed$");
 }
 
 ProteinStore::~ProteinStore()
@@ -45,7 +46,7 @@ ProteinStore::~ProteinStore()
 ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
 
     std::pair<std::map< QString, ProteinXtpSp>::iterator,bool> ret = _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(peptide_in.get()->getAccession(),peptide_in));
-    
+
     if (ret.second) {
         setProteinInformations(ret.first->second);
     }
@@ -54,11 +55,14 @@ ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
 }
 
 void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
+    qDebug() << "ProteinStore::setProteinInformations begin";
     QString accession = peptide_in.get()->getAccession();
     if (_regexp_contaminant.indexIn(accession, 0)>-1) {
+        qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
         peptide_in.get()->setIsContaminant(true);
     }
     if (_regexp_decoy.indexIn(accession, 0)>-1) {
         peptide_in.get()->setIsDecoy(true);
     }
+    qDebug() << "ProteinStore::setProteinInformations end";
 }

src/utils/proteinstore.h

@@ -39,6 +39,7 @@
 
 class ProteinStore
 {
+public:
     ProteinStore();
     ~ProteinStore();