compute FDR on peptide evidence instead of peptide match

src/core/identificationgroup.cpp

@@ -89,17 +89,6 @@ unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState st
 }
 
 
-unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
-    unsigned int i=0;
-    for (auto & p_protein_match : _protein_match_list) {
-        if (p_protein_match->getValidationState() >= state) {
-            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
-                i+=p_protein_match->countPeptideMatch(state);
-            }
-        }
-    }
-    return i;
-}
 unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state) const {
     return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
         if ((p_protein_match->getProteinXtpSp().get()->isDecoy()) && (p_protein_match->getValidationState() >= state)) {
@@ -111,6 +100,28 @@ unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state)
     });
 }
 
+unsigned int IdentificationGroup::countPeptideEvidence(ValidationState state) const {
+    std::set<const PeptideEvidence *> peptide_evidence_set;
+    for (auto & p_protein_match : _protein_match_list) {
+        if (p_protein_match->getValidationState() >= state) {
+            p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
+        }
+    }
+    return peptide_evidence_set.size();
+}
+
+unsigned int IdentificationGroup::countDecoyPeptideEvidence(ValidationState state) const {
+    std::set<const PeptideEvidence *> peptide_evidence_set;
+    for (auto & p_protein_match : _protein_match_list) {
+        if (p_protein_match->getValidationState() >= state) {
+            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+                p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
+            }
+        }
+    }
+    return peptide_evidence_set.size();
+}
+
 unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
     unsigned int i=0;
     for (auto & p_protein_match : _protein_match_list) {
@@ -121,6 +132,17 @@ unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const
     return i;
 }
 
+unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
+    unsigned int i=0;
+    for (auto & p_protein_match : _protein_match_list) {
+        if (p_protein_match->getValidationState() >= state) {
+            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+                i+=p_protein_match->countPeptideMatch(state);
+            }
+        }
+    }
+    return i;
+}
 unsigned int IdentificationGroup::countProteinMatch(ValidationState state) const {
     return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
         if (p_protein_match->getValidationState() >= state) {

src/core/identificationgroup.h

@@ -70,6 +70,14 @@ public:
     /** @brief count decoy proteins
      * */
     unsigned int countDecoyProteinMatch(ValidationState state) const;
+    
+    /** @brief count peptide evidences (peptide spectrum match + identification engine)
+     * */
+    unsigned int countPeptideEvidence(ValidationState state) const;
+
+    /** @brief count peptide evidences (peptide spectrum match + identification engine)
+     * */
+    unsigned int countDecoyPeptideEvidence(ValidationState state) const;
 
     /** @brief count peptide match (peptide spectrum match + protein match)
      * */

src/core/proteinmatch.cpp

@@ -128,7 +128,7 @@ void ProteinMatch::setChecked(bool arg1) {
 }
 
 void ProteinMatch::addPeptideMatch(const PeptideMatch & peptide_match) {
-    //qDebug() << "ProteinMatch::addPeptideMatch begin " << peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString(); 
+    //qDebug() << "ProteinMatch::addPeptideMatch begin " << peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->toAbsoluteString();
     _peptide_match_list.push_back(peptide_match);
 }
 
@@ -461,3 +461,12 @@ void ProteinMatch::collectMhDelta(std::set< const PeptideEvidence *> & already_c
         }
     }
 }
+
+void ProteinMatch::collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const {
+    for (auto & peptide_match : _peptide_match_list) {
+        const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
+        if (p_peptide_evidence->getValidationState() >= state) {
+            peptide_evidence_set.insert(p_peptide_evidence);
+        }
+    }
+}

src/core/proteinmatch.h

@@ -119,6 +119,10 @@ public:
      */
     void collectMhDelta(std::set<const PeptideEvidence *> & already_counted, std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
     
+    /** @brief collect distinct peptide evidences
+     */
+    void collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const;
+    
     /** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
      * @param state validation state of peptides to count
      * @param p_msrun_id count within the specified sample

src/gui/project_view/projectwindow.cpp

@@ -215,10 +215,8 @@ void ProjectWindow::computeFdr(ValidationState state) {
         for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
             total_prot += identification_group->countProteinMatch(state);
             false_prot += identification_group->countDecoyProteinMatch(state);
-            //total_peptide += identification_group->countPeptideMatch(state);
-            //false_peptide += identification_group->countDecoyPeptideMatch(state);
-            total_peptide += identification_group->countPeptideMassSample(state);
-            false_peptide += identification_group->countDecoyPeptideMassSample(state);
+            total_peptide += identification_group->countPeptideEvidence(state);
+            false_peptide += identification_group->countDecoyPeptideEvidence(state);
         }
         if (state == ValidationState::grouped) {
             ui->grouped_protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',2)));