get protein coverage

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/identificationgroup.h

@@ -47,8 +47,12 @@ public:
     std::vector<ProteinMatch *> & getProteinMatchList();
     void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
     
-    
+    /** @brief count valid proteins
+     * */    
     size_t countValid()const;
+    
+    /** @brief count valid and manually checked proteins
+     * */    
     size_t countValidAndChecked()const;
 
 

src/core/peptidematch.cpp

@@ -51,6 +51,10 @@ void PeptideMatch::setExperimentalMass(pappso::pappso_double exp_mass) {
 void PeptideMatch::setStart(unsigned int start) {
     _start =start;
 }
+
+unsigned int PeptideMatch::getStart() const {
+    return _start;
+}
 void PeptideMatch::setCharge(unsigned int charge) {
     _charge =charge;
 }

src/core/peptidematch.h

@@ -39,7 +39,13 @@ public :
     void setRetentionTime(pappso::pappso_double rt);
     void setEvalue(pappso::pappso_double evalue);
     void setExperimentalMass(pappso::pappso_double exp_mass);
+    
+           /** @brief start position on the protein sequence (starts at 1, not 0)
+     * */
     void setStart(unsigned int start);
+          /** @brief get start position on the protein sequence (starts at 1, not 0)
+     * */
+    unsigned int getStart() const;
     void setCharge(unsigned int charge);
     void setPeptideSp (pappso::PeptideSp peptide);
     void setIdentificationDataSource(IdentificationDataSource* identification_source);
@@ -71,7 +77,7 @@ private :
     pappso::pappso_double _rt;
     pappso::pappso_double _evalue;
     pappso::pappso_double _exp_mass;
-    unsigned int _start;
+    unsigned int _start=0;
     unsigned int _charge;
     IdentificationDataSource* _p_identification_source = nullptr;
 

src/core/proteinmatch.cpp

@@ -130,3 +130,25 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
     return _sp_grp_protein;
 }
 
+
+    pappso::pappso_double ProteinMatch::getCoverage() const {
+        size_t prot_size = _protein_sp.get()->size();
+        if (prot_size == 0) return 0;
+        bool cover_bool[prot_size] = {false};
+        for (auto & p_peptide_match : _peptide_match_list) {
+            if (p_peptide_match->isValidAndChecked()) {
+                size_t size = p_peptide_match->getPeptideSp().get()->size();
+                size_t offset = p_peptide_match->getStart()-1;
+                if (offset >= 0) {
+                    for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
+                        cover_bool[offset] = true;
+                    }
+                }
+            }
+        }
+        size_t count = 0;
+        for (size_t i=0; i < prot_size; i++) {
+                        if(cover_bool[i]) count++;
+                    }
+        return ((pappso::pappso_double)count/ (pappso::pappso_double)prot_size);
+    }

src/core/proteinmatch.h

@@ -40,6 +40,7 @@ public:
     const ProteinXtpSp & getProteinXtpSp() const;
     void setEvalue(pappso::pappso_double evalue);
     pappso::pappso_double getEvalue() const;
+    pappso::pappso_double getCoverage() const;
     void setProteinXtpSp(ProteinXtpSp protein_sp);
     void addPeptideMatch(PeptideMatch * peptide_match);
     std::vector<PeptideMatch *> & getPeptideMatchList();