change in mass delta compute : a peptide evidence is only counted once

src/core/identificationgroup.cpp

@@ -209,11 +209,11 @@ std::size_t IdentificationGroup::countSubGroup()const {
 }
 
 void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
-    std::set<PeptideEvidence *> already_counted;
+    std::set<const PeptideEvidence *> already_counted;
     for (auto & p_protein_match : _protein_match_list) {
         if (p_protein_match->getValidationState() >= state) {
             if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) {
-                p_protein_match->collectMhDelta(delta_list, unit, state);
+                p_protein_match->collectMhDelta(already_counted, delta_list, unit, state);
             }
         }
     }

src/core/proteinmatch.cpp

@@ -445,17 +445,19 @@ void ProteinMatch::setGroupInstance(GroupStore & group_store) {
 }
 
 
-void ProteinMatch::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
+void ProteinMatch::collectMhDelta(std::set< const PeptideEvidence *> & already_counted, std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
     for (auto & peptide_match : _peptide_match_list) {
-        if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
-            pappso::pappso_double diff = peptide_match.getPeptideEvidence()->getDeltaMass();
+        const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
+        if ((p_peptide_evidence->getValidationState() >= state)&&(already_counted.find(p_peptide_evidence) == already_counted.end())) {
+            pappso::pappso_double diff = p_peptide_evidence->getDeltaMass();
             if (unit == pappso::PrecisionUnit::ppm) {
                 while (diff < -0.5) {
                     diff = diff + pappso::DIFFC12C13;
                 }
-                diff = (diff / peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+                diff = (diff / p_peptide_evidence->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
             }
             delta_list.push_back(diff);
+            already_counted.insert(p_peptide_evidence);
         }
     }
 }

src/core/proteinmatch.h

@@ -23,6 +23,7 @@
 
 #include <QColor>
 #include <vector>
+#include <set>
 #include <pappsomspp/types.h>
 #include "proteinxtp.h"
 #include "peptidematch.h"
@@ -113,7 +114,10 @@ public:
     * */
     void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
 
-    void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
+    /** @brief collect mass delta between theoretical mass and observed mass
+     * each peptide evidence is only counted once
+     */
+    void collectMhDelta(std::set<const PeptideEvidence *> & already_counted, std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
     
     /** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
      * @param state validation state of peptides to count