diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index a2c3f253a20e4a960cbf65d675249ef6b1bbac11..df013590e923439ba2a8d63112f149e4f37d2730 100644
--- a/src/core/identificationgroup.cpp
+++ b/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) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 767f8cc25ff258593a97409a8530e5292a00c0ff..3eaf8565c3d30eb615d1dceff0f3a94f931d308f 100644
--- a/src/core/identificationgroup.h
+++ b/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
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index c95a4d48e31f568243172e2d6336caf5b1a105bc..81706facecd72cd126d2f2a660daeb7f5383a5fd 100644
--- a/src/core/peptidematch.cpp
+++ b/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;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index bd150ed5cd59c70137e9e72fceacec4704cf9a8a..a9f67e11253738b2dde03aca67fb36daec8ca6ae 100644
--- a/src/core/peptidematch.h
+++ b/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;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 0df923cc2980f86fba9cb8beb926b83bd0219410..792634523eba9025bdad1dedd669f870461d1f22 100644
--- a/src/core/proteinmatch.cpp
+++ b/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]);
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 3044d8d706033f32c32a22b0499da6a7a611bc09..b2501074db9e4aecda17ddaac2f4578633f791a9 100644
--- a/src/core/proteinmatch.h
+++ b/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;
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index f2a57aa78fc958bea9e092a805a2e9ed303208db..f9c63fed086f588e9a87eae0a681660611413397 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/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));
}
diff --git a/src/utils/types.h b/src/utils/types.h
index e3cbf9b1c642371f7897e8ce478094b35b9e8ca9..c87465c675df83f7c3a28f1b2a6b5cc6ebe8e357 100644
--- a/src/utils/types.h
+++ b/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