FDR computation OK

src/core/identificationgroup.cpp

@@ -42,6 +42,17 @@ IdentificationGroup::~IdentificationGroup()
 }
 
 
+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::countDecoyProtein(ValidationState state) const {
     unsigned int i=0;
     for (auto & p_protein_match : _protein_match_list) {
@@ -67,6 +78,16 @@ unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const
     return i;
 }
 
+unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
+    unsigned int i=0;
+    for (auto & p_protein_match : _protein_match_list) {
+        if (p_protein_match->getValidationState() == state) {
+            i+=p_protein_match->countPeptideMatch(state);
+        }
+    }
+    return i;
+}
+
 unsigned int IdentificationGroup::countProtein(ValidationState state) const {
     unsigned int i=0;
     if (state == ValidationState::grouped) {

src/core/identificationgroup.h

@@ -74,7 +74,13 @@ public:
     unsigned int countProtein(ValidationState state) const;
     /** @brief count decoy proteins
      * */    
-    unsigned int countDecoyProtein(ValidationState state) const;
+    unsigned int countDecoyProtein(ValidationState state) const;   
+    /** @brief count peptide match
+     * */    
+    unsigned int countPeptideMatch(ValidationState state) const;
+    /** @brief count decoy peptide match
+     * */    
+    unsigned int countDecoyPeptideMatch(ValidationState state) const;
 
 
     /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks

src/core/peptidematch.cpp

@@ -69,6 +69,17 @@ void PeptideMatch::setChecked(bool arg1) {
     _checked = arg1;
 }
 
+ValidationState PeptideMatch::getValidationState() const {
+    if (isValid()) {
+        return ValidationState::valid;
+    } else if (isValidAndChecked()) {
+        return ValidationState::validAndChecked;
+    } else if (isGrouped()) {
+        return ValidationState::grouped;
+    }
+    return ValidationState::notValid;
+}
+
 bool PeptideMatch::isValid() const {
     return _proxy_valid;
 }

src/core/peptidematch.h

@@ -75,6 +75,8 @@ public :
     /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
       */
     pappso::mz getDeltaMass() const;
+    
+    ValidationState getValidationState() const;
 
 private :
     MsRun * _msrunid_sp;

src/core/proteinmatch.cpp

@@ -43,7 +43,16 @@ ProteinMatch::~ProteinMatch()
         it++;
     }
 }
-
+ValidationState ProteinMatch::getValidationState() const {
+    if (isValid()) {
+        return ValidationState::valid;
+    } else if (isValidAndChecked()) {
+        return ValidationState::validAndChecked;
+    } else if (isGrouped()) {
+        return ValidationState::grouped;
+    }
+    return ValidationState::notValid;
+}
 bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
     if (peptide_match == nullptr) return false;
     for (auto & p_peptide_match : _peptide_match_list) {
@@ -166,6 +175,18 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
     return _sp_grp_protein;
 }
 
+
+unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
+    return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch * p_peptide_match) {
+        if (p_peptide_match->getValidationState() == state) {
+            return true;
+        }
+        else              {
+            return false;
+        }
+    });
+}
+
 size_t ProteinMatch::countValidSpectrum()const {
     return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * p_peptide_match) {
         return (p_peptide_match->isValid());
@@ -312,7 +333,7 @@ const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_loca
                 }
                 else {
                     sequence_html.append(QString("</span>"));
-		    i--;
+                    i--;
                     break;
                 }
             }
@@ -323,9 +344,9 @@ const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_loca
             i++;
             for (; i < prot_size; i++) {
                 if (highlight_bool[i]) {
-		  i--;
-		  break;
-		}
+                    i--;
+                    break;
+                }
                 if(cover_bool[i]) {
                     sequence_html.append(sequence[i]);
                 }

src/core/proteinmatch.h

@@ -75,6 +75,9 @@ public:
     bool isValidAndChecked() const;
     bool isGrouped() const;
 
+    ValidationState getValidationState() const;
+    unsigned int countPeptideMatch(ValidationState state) const;
+
     /** @brief count valid spectrums
      * */
     size_t countValidSpectrum()const;

src/gui/project_view/projectwindow.cpp

@@ -151,9 +151,11 @@ void ProjectWindow::computeFdr(ValidationState state) {
     pappso::pappso_double total_peptide=0;
     pappso::pappso_double false_peptide=0;
     for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
-        //total_peptide += identification_group->countPeptideMatch(state);
-        //false_peptide += identification_group->countDecoyPeptideMatch(state);
+        total_peptide += identification_group->countPeptideMatch(state);
+        false_peptide += identification_group->countDecoyPeptideMatch(state);
     }
+    qDebug() << "ProjectWindow::computeFdr false_peptide=" <<false_peptide;
+    qDebug() << "ProjectWindow::computeFdr total_peptide=" <<total_peptide;
     ui->peptide_fdr_label->setText(QString("%1 %").arg(false_peptide/total_peptide));
 }
 

src/utils/types.h

@@ -51,6 +51,7 @@ enum class MzFormat {
  */
 
 enum class ValidationState {
+    notValid,///< notValid : automatic filter validation failed
      valid, ///< valid : automatic filter validation passed
      validAndChecked, ///< validAndChecked : automatic filter validation passed + manual checking
      grouped, ///< grouped : automatic filter validation passed + manual checking + grouped