add option to filter spectra by peptide (OpenMS#7021)

* add option to filter spectra by peptide

* Update src/topp/IDFilter.cpp

src/topp/IDFilter.cpp

@@ -221,6 +221,8 @@ class TOPPIDFilter :
     setMinInt_("best:n_spectra", 0);
     registerIntOption_("best:n_peptide_hits", "<integer>", 0, "Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0).", false);
     setMinInt_("best:n_peptide_hits", 0);
+    registerStringOption_("best:spectrum_per_peptide", "<String>", "false", "Keep one spectrum per peptide. Value determines if same sequence but different charges or modifications are treated as separate peptides or the same peptide. (default: false = filter disabled).", false);
+    setValidStrings_("best:spectrum_per_peptide", {"false", "sequence", "sequence+charge", "sequence+modification", "sequence+charge+modification"});    
     registerIntOption_("best:n_protein_hits", "<integer>", 0, "Keep only the 'n' highest scoring protein hits (for n > 0).", false);
     setMinInt_("best:n_protein_hits", 0);
     registerFlag_("best:strict", "Keep only the highest scoring peptide hit.\n"
@@ -607,6 +609,25 @@ class TOPPIDFilter :
       IDFilter::keepNBestHits(peptides, best_n_pep);
     }
 
+    String spectrum_per_peptide = getStringOption_("best:spectrum_per_peptide");
+    if (spectrum_per_peptide != "false")
+    {
+      OPENMS_LOG_INFO << "Keeping best spectrum per " << spectrum_per_peptide << endl;
+      if (spectrum_per_peptide == "sequence") // group by sequence and return best spectrum (->smallest number of spectra)
+      {
+        IDFilter::keepBestPerPeptide(peptides, true, true, 1);
+      } else if (spectrum_per_peptide == "sequence+modification")
+      {
+        IDFilter::keepBestPerPeptide(peptides, false, true, 1);
+      } else if (spectrum_per_peptide == "sequence+charge")
+      {
+        IDFilter::keepBestPerPeptide(peptides, true, false, 1);
+      } else if (spectrum_per_peptide == "sequence+charge+modification") // group by sequence, modificationm, charge combination and return best spectrum (->largest number of spectra)
+      {
+        IDFilter::keepBestPerPeptide(peptides, false, false, 1);
+      }
+    }
+
     Int min_rank = 0, max_rank = 0;
     if (parseRange_(getStringOption_("best:n_to_m_peptide_hits"), min_rank,
                     max_rank))