count spectrum and unique sequences

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;
 }
 

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;

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();
+}

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;
 
 };
 

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++) {

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:

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() {

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")

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());
         }
 

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;
 }