diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index da24a53c99ba3b66cff75e0ffa572783b2d52d5b..49fedbac14aa642656cf2f4a03834d2e03f8e56a 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -59,7 +59,7 @@ void PeptideMatch::setCharge(unsigned int charge) {
_charge =charge;
}
-void PeptideMatch::setPeptideSp (pappso::PeptideSp peptide) {
+void PeptideMatch::setPeptideXtpSp (PeptideXtpSp peptide) {
_peptide_sp = peptide;
}
@@ -93,7 +93,7 @@ unsigned int PeptideMatch::getCharge() const {
return _charge;
}
-const pappso::PeptideSp & PeptideMatch::getPeptideSp() const {
+const PeptideXtpSp & PeptideMatch::getPeptideXtpSp() const {
return _peptide_sp;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index c1eddbb63105163562491024040563c03f7af7b4..61fe5c1c0bfd6174a2b39e43903421e8ff875434 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -25,7 +25,7 @@
#define PEPTIDEMATCH_H
#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/types.h>
-#include <pappsomspp/peptide/peptide.h>
+#include "peptidextp.h"
#include "identification_sources/identificationdatasource.h"
#include "automaticfilterparameters.h"
@@ -49,7 +49,7 @@ public :
* */
unsigned int getStart() const;
void setCharge(unsigned int charge);
- void setPeptideSp (pappso::PeptideSp peptide);
+ void setPeptideXtpSp (PeptideXtpSp peptide);
void setIdentificationDataSource(IdentificationDataSource* identification_source);
void setChecked(bool arg1);
bool isChecked() const;
@@ -61,7 +61,7 @@ public :
unsigned int getScan() const;
pappso::pappso_double getRetentionTime() const;
unsigned int getCharge() const;
- const pappso::PeptideSp & getPeptideSp() const;
+ const PeptideXtpSp & getPeptideXtpSp() const;
pappso::pappso_double getEvalue() const;
void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
@@ -75,7 +75,7 @@ private :
pappso::MsRunIdSp _msrunid_sp;
unsigned int _scan;
pappso::GrpPeptideSp _sp_grp_peptide;
- pappso::PeptideSp _peptide_sp;
+ PeptideXtpSp _peptide_sp;
pappso::pappso_double _rt;
pappso::pappso_double _evalue;
pappso::pappso_double _exp_mass;
diff --git a/src/core/peptidextp.cpp b/src/core/peptidextp.cpp
index 87db6ca7926bb8bc166c91f480eb6ae587095d1e..f1a4c51062539e7830a5981531721d2431744955 100644
--- a/src/core/peptidextp.cpp
+++ b/src/core/peptidextp.cpp
@@ -42,3 +42,8 @@ PeptideXtp::~PeptideXtp()
PeptideXtpSp PeptideXtp::makePeptideXtpSp() const {
return std::make_shared<PeptideXtp>(*this);
}
+
+
+pappso::mz PeptideXtp::getGroupingMass() const {
+ return getMass();
+}
diff --git a/src/core/peptidextp.h b/src/core/peptidextp.h
index 8b8ddd55f5d4ed11aa9f8bc6521d86d53e81ddf6..4b428681ad5a1d356535934af9e34f36cc8620be 100644
--- a/src/core/peptidextp.h
+++ b/src/core/peptidextp.h
@@ -40,6 +40,11 @@ public:
~PeptideXtp();
PeptideXtpSp makePeptideXtpSp() const;
+ /** \brief get the tehoretical mass to use for grouping
+ * This mass might be different than the true peptide mass to recognize that a tagged
+ * peptide with taget modification is a light, inter or heavy version of the same peptide
+ */
+ pappso::mz getGroupingMass() const;
};
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index f035edbc52f26df9f71945d246ce5aa9cb845855..83871216e2ee3cb3713191efea442467e8fed56b 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -24,6 +24,7 @@
#include "proteinmatch.h"
#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/grouping/grpprotein.h>
+#include <set>
ProteinMatch::ProteinMatch()
@@ -136,6 +137,26 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
return _sp_grp_protein;
}
+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());
+ });
+}
+
+size_t ProteinMatch::countValidAndCheckedSpectrum()const {
+ return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * p_peptide_match) {
+ return (p_peptide_match->isValidAndChecked());
+ });
+}
+size_t ProteinMatch::countUniqueSequence()const {
+ std::set<QString> sequence_list;
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->isValidAndChecked()) {
+ sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+ }
+ }
+ return sequence_list.size();
+}
pappso::pappso_double ProteinMatch::getCoverage() const {
size_t prot_size = _protein_sp.get()->size();
@@ -144,7 +165,7 @@ pappso::pappso_double ProteinMatch::getCoverage() const {
bool cover_bool[prot_size] = {false};
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->isValidAndChecked()) {
- size_t size = p_peptide_match->getPeptideSp().get()->size();
+ size_t size = p_peptide_match->getPeptideXtpSp().get()->size();
size_t offset = p_peptide_match->getStart();
if (offset >= 0) {
for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 55ceae9ac26a3610bb27d5e210272f6805c3d340..ea42eba339682c61d6f9287f67d8f9d4747a8c73 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -50,12 +50,25 @@ public:
bool isValid() const;
bool isValidAndChecked() const;
+ /** @brief count valid spectrums
+ * */
+ size_t countValidSpectrum()const;
+
+ /** @brief count valid and manually checked spectrums
+ * */
+ size_t countValidAndCheckedSpectrum()const;
+ /** @brief count unique identified sequences (from valid and cheked spectrums)
+ * */
+ size_t countUniqueSequence()const;
+
+
+
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
-
+
const pappso::GrpProteinSp & getGrpProteinSp() const;
private:
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index 8368af9d7c0868f1123c09bf8c3db25e61206cb4..b9d690fbbe89da467b5cb12535b01204858b2f4d 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -44,7 +44,7 @@ pappso::GrpProteinSp & GroupingPeptideMass::getGrpProteinSp(ProteinMatch* p_prot
}
pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) {
- return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_match->getPeptideSp().get()->getSequence(), p_peptide_match->getPeptideSp().get()->getMass());
+ return _p_grp_experiment->setGrpPeptide(proteinSp,p_peptide_match->getPeptideXtpSp().get()->getSequence(), p_peptide_match->getPeptideXtpSp().get()->getGroupingMass());
}
void GroupingPeptideMass::startGrouping() {
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 261e871b6f062f5cca58c4f573681fd73560a71c..933a843dc1f7b99acbeaa98d27524cb9c70bd6f5 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -169,7 +169,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
return QVariant ((quint8) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
}
if (col ==6) {
- return _p_protein_match->getPeptideMatchList().at(row)->getPeptideSp().get()->getSequence();
+ return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getSequence();
}
}
return QString("Row%1, Column%2")
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 711528c84d68b0503800ab83cfd2107e01f57ef4..2b210092aa06f4d18f1c2a17824c831f0fe50108 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -127,7 +127,7 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
return 0;
}
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
- return 7;
+ return 8;
}
QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -149,6 +149,8 @@ QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation,
case 5:
return QString("spectrum");
case 6:
+ return QString("unique");
+ case 7:
return QString("coverage");
}
}
@@ -203,9 +205,12 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
}
if (col == 5) {
- return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
+ return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->countValidAndCheckedSpectrum());
}
if (col == 6) {
+ return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->countUniqueSequence());
+ }
+ if (col == 7) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getCoverage());
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index bfa87f107e6b45a57db1ecf5823735c0fc3e606f..3dd3dae81a413ddf3b61351726022a9e1d9d0a0c 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -280,7 +280,7 @@ bool XpipSaxHandler::endElement_peptide() {
PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
- _p_peptide_match->setPeptideSp(peptide_const);
+ _p_peptide_match->setPeptideXtpSp(peptide_const);
return true;
}