wip : protein store

src/CMakeLists.txt

@@ -67,6 +67,7 @@ SET(CPP_FILES
   grouping/groupingpeptidemass.cpp
   input/xpipsaxhandler.cpp
   utils/peptidestore.cpp
+  utils/proteinstore.cpp
   utils/readspectrum.cpp
 )
 

src/core/identificationgroup.cpp

@@ -88,4 +88,7 @@ void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
     }
     
     _p_grp_experiment->startGrouping();
+    
+    //remove contaminant groups
+    // renumbering
 }

src/core/proteinxtp.cpp

@@ -48,3 +48,16 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
     return std::make_shared<ProteinXtp>(*this);
 }
 
+   
+    void ProteinXtp::setIsContaminant(bool conta) {
+        _is_contaminant = conta;
+    }
+    void ProteinXtp::setIsDecoy(bool conta){
+        _is_decoy = conta;
+    }
+    bool ProteinXtp::getIsContaminant() const{
+        return _is_contaminant;
+    }
+    bool ProteinXtp::getIsDecoy() const{
+        return _is_decoy;
+    }

src/core/proteinxtp.h

@@ -32,7 +32,7 @@ class ProteinXtp;
 
 /** \brief shared pointer on a Protein object
  */
-typedef std::shared_ptr<const ProteinXtp> ProteinXtpSp;
+typedef std::shared_ptr<ProteinXtp> ProteinXtpSp;
 
 class ProteinXtp : public pappso::Protein {
 public:
@@ -43,6 +43,11 @@ public:
 
 
     ProteinXtpSp makeProteinXtpSp() const;
+    
+    void setIsContaminant(bool conta);
+    void setIsDecoy(bool conta);
+    bool getIsContaminant() const;
+    bool getIsDecoy() const;
 
 private:
     SequenceDatabase * _p_sequence_database;

src/utils/proteinstore.cpp

@@ -30,16 +30,35 @@
 #include "proteinstore.h"
 
 
+ProteinStore::ProteinStore()
+{
+_regexp_contaminant.setPattern("([KR])([^P])");
+
+_regexp_decoy.setPattern(".*\\|reversed$");
+}
+
+ProteinStore::~ProteinStore()
+{
+
+}
+
 ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
 
-    std::pair<std::unordered_map< QString, ProteinXtpSp>::iterator,bool> ret = _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(peptide_in.get()->getAccession(),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);
     }
-    return ret.first->second;
+    return (ret.first->second);
 
 }
 
 void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
+    QString accession = peptide_in.get()->getAccession();
+    if (_regexp_contaminant.indexIn(accession, 0)>-1) {
+        peptide_in.get()->setIsContaminant(true);
+    }
+    if (_regexp_decoy.indexIn(accession, 0)>-1) {
+        peptide_in.get()->setIsDecoy(true);
+    }
 }

src/utils/proteinstore.h

@@ -34,10 +34,13 @@
 
 #include "../core/proteinxtp.h"
 #include <QString>
-#include <unordered_map>
+#include <QRegExp>
+#include <map>
 
 class ProteinStore
 {
+    ProteinStore();
+    ~ProteinStore();
     
     ProteinXtpSp & getInstance(ProteinXtpSp & protein_in);
 
@@ -45,7 +48,11 @@ private :
     void setProteinInformations(ProteinXtpSp & protein_in);
 private :
   
-    std::unordered_map<QString, ProteinXtpSp> _map_accession_protein_list;
+    std::map<QString, ProteinXtpSp> _map_accession_protein_list;
+    /** \brief recognize decoy accession */
+    QRegExp _regexp_decoy;
+    /** \brief recognize contaminant accession */
+    QRegExp _regexp_contaminant;
 
 };