write only grouped peptides

src/grouping/groupinggroup.h

@@ -74,6 +74,7 @@ public:
     
      /** @brief get the list of peptide match included in this group
       * warning : it only contains the first protein representant in one subgroup
+      * use a double loop with getProteinMatchList to scan every peptide match
      * */
     std::vector<const PeptideMatch *> getPeptideMatchList() const;
     

src/output/proticdbml.cpp

@@ -437,7 +437,7 @@ void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
     std::vector <ProticPeptideHit> protic_peptide_hit_list;
 
     for  (const ProteinMatch* p_protein_match : p_group->getProteinMatchList()) {
-        for  (const PeptideMatch* p_peptide_match : p_protein_match->getPeptideMatchList()) {
+        for  (const PeptideMatch* p_peptide_match : p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
             ProticPeptideHit protic_peptide_hit = {getProticPeptideHitKey(p_peptide_match), p_peptide_match};
             protic_peptide_hit_list.push_back(protic_peptide_hit);
         }