NSAF indice handles labeling methods

src/core/identificationgroup.cpp

@@ -55,14 +55,15 @@ IdentificationGroup::getGroupStore() const
 }
 
 pappso::pappso_double
-IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id) const
+IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id,
+                                         const Label *p_label) const
 {
   pappso::pappso_double nsaf_sum = 0;
   for(auto &p_protein_match : _protein_match_list)
     {
       if(p_protein_match->getValidationState() >= ValidationState::grouped)
         {
-          nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
+          nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id, p_label);
         }
     }
   return nsaf_sum;
@@ -130,7 +131,8 @@ unsigned int
 IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
 {
   return std::count_if(
-    _protein_match_list.begin(), _protein_match_list.end(),
+    _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))
@@ -209,7 +211,8 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
 unsigned int
 IdentificationGroup::countProteinMatch(ValidationState state) const
 {
-  return std::count_if(_protein_match_list.begin(), _protein_match_list.end(),
+  return std::count_if(_protein_match_list.begin(),
+                       _protein_match_list.end(),
                        [state](const ProteinMatch *p_protein_match) {
                          if(p_protein_match->getValidationState() >= state)
                            {
@@ -302,8 +305,8 @@ IdentificationGroup::addIdentificationDataSourceP(
   IdentificationDataSource *p_identification_source)
 {
   addMsRunSp(p_identification_source->getMsRunSp());
-  auto it = std::find(_id_source_list.begin(), _id_source_list.end(),
-                      p_identification_source);
+  auto it = std::find(
+    _id_source_list.begin(), _id_source_list.end(), p_identification_source);
   if(it == _id_source_list.end())
     {
       _id_source_list.push_back(p_identification_source);
@@ -353,7 +356,8 @@ IdentificationGroup::countSubGroup() const
 
 void
 IdentificationGroup::collectMhDelta(
-  std::vector<pappso::pappso_double> &delta_list, pappso::PrecisionUnit unit,
+  std::vector<pappso::pappso_double> &delta_list,
+  pappso::PrecisionUnit unit,
   ValidationState state) const
 {
   std::set<const PeptideEvidence *> peptide_evidence_list;
@@ -466,7 +470,9 @@ IdentificationGroup::getProteinFdr(ValidationState state) const
 void
 IdentificationGroup::getSameXicPeptideEvidenceList(
   std::vector<const PeptideEvidence *> &peptide_evidence_list,
-  const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+  const MsRun *p_msrun,
+  const PeptideXtp *p_peptide,
+  unsigned int charge) const
 {
   if(!contains(p_msrun))
     return;
@@ -475,8 +481,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList(
       if(p_msrun == p_identification_source->getMsRunSp().get())
         {
           p_identification_source->getPeptideEvidenceStore()
-            .getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun,
-                                           p_peptide, charge);
+            .getSameXicPeptideEvidenceList(
+              peptide_evidence_list, p_msrun, p_peptide, charge);
         }
     }
 }

src/core/identificationgroup.h

@@ -62,7 +62,9 @@ class IdentificationGroup
    * Warning: this is not NSAF, just a part
    * @param p_msrun_id pointer on the msrun to get NSAF.
    * */
-  pappso::pappso_double computeProtoNsafSum(const MsRun *p_msrun_id) const;
+  pappso::pappso_double
+  computeProtoNsafSum(const MsRun *p_msrun_id,
+                      const Label *p_label = nullptr) const;
 
   /** @brief count groups
    * */
@@ -152,7 +154,8 @@ class IdentificationGroup
    * each peptide evidence is only counted once
    */
   void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
-                      pappso::PrecisionUnit unit, ValidationState state) const;
+                      pappso::PrecisionUnit unit,
+                      ValidationState state) const;
 
 
   /** @brief look for a peptide in the same XIC
@@ -163,7 +166,8 @@ class IdentificationGroup
    */
   void getSameXicPeptideEvidenceList(
     std::vector<const PeptideEvidence *> &peptide_evidence_list,
-    const MsRun *p_msrun, const PeptideXtp *p_peptide,
+    const MsRun *p_msrun,
+    const PeptideXtp *p_peptide,
     unsigned int charge) const;
 
   private:

src/core/proteinmatch.cpp

@@ -434,8 +434,10 @@ ProteinMatch::countPeptideMassCharge(ValidationState state,
                 {
                   if(p_label != nullptr)
                     {
-                      if(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getLabel() ==
-                         p_label)
+                      if(peptide_match.getPeptideEvidence()
+                           ->getPeptideXtpSp()
+                           .get()
+                           ->getLabel() == p_label)
                         {
                           sequence_list.insert(
                             QString("%1-%2-%3")
@@ -559,7 +561,8 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
 }
 pappso::pappso_double
 ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
-                      const MsRun *p_msrun_id) const
+                      const MsRun *p_msrun_id,
+                      const Label *p_label) const
 {
   if(proto_nsaf_sum == 0)
     {
@@ -568,11 +571,11 @@ ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
           "Error computing NSAF for protein %1 :\nproto_nsaf_sum is null")
           .arg(this->getProteinXtpSp().get()->getAccession()));
     }
-  return (getProtoNsaf(p_msrun_id) / proto_nsaf_sum);
+  return (getProtoNsaf(p_msrun_id, p_label) / proto_nsaf_sum);
 }
 
 pappso::pappso_double
-ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
+ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id, const Label *p_label) const
 {
   try
     {
@@ -582,8 +585,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
             QObject::tr("protein has no amino acid sequence"));
         }
       pappso::pappso_double proto_nsaf =
-        (pappso::pappso_double)countSampleScan(ValidationState::validAndChecked,
-                                               sp_msrun_id) /
+        (pappso::pappso_double)countSampleScan(
+          ValidationState::validAndChecked, sp_msrun_id, p_label) /
         (pappso::pappso_double)_protein_sp.get()->size();
       return proto_nsaf;
     }
@@ -617,11 +620,11 @@ ProteinMatch::getPAI(const MsRun *sp_msrun_id, const Label *p_label) const
 }
 
 pappso::pappso_double
-ProteinMatch::getEmPAI(const MsRun *sp_msrun_id) const
+ProteinMatch::getEmPAI(const MsRun *sp_msrun_id, const Label *p_label) const
 {
   // compute emPAI, Ishihama 2005
   pappso::pappso_double value =
-    std::pow(10.0, getPAI(sp_msrun_id)) - (pappso::pappso_double)1.0;
+    std::pow(10.0, getPAI(sp_msrun_id, p_label)) - (pappso::pappso_double)1.0;
 
   return value;
 }

src/core/proteinmatch.h

@@ -72,7 +72,8 @@ class ProteinMatch
    * Warning: this is not NSAF, just a part
    * @param p_msrun_id pointer on the msrun to get NSAF.
    * */
-  pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id) const;
+  pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id,
+                                     const Label *p_label = nullptr) const;
 
   /** @brief compute NSAF within msrun : normalized spectral abundance factor
    * (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing
@@ -84,7 +85,8 @@ class ProteinMatch
    * @param p_msrun_id pointer on the msrun to get NSAF
    * */
   pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum,
-                                const MsRun *p_msrun_id) const;
+                                const MsRun *p_msrun_id,
+                                const Label *p_label = nullptr) const;
 
   /** @brief compute Protein Abundance Index (PAI) within sample
    * PAI computation (Rappsilber et al. 2002)
@@ -95,7 +97,8 @@ class ProteinMatch
   /** @brief compute emPAI within sample
    * Ishihama 2005
    * */
-  pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr) const;
+  pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr,
+                                 const Label *p_label     = nullptr) const;
 
   void setProteinXtpSp(ProteinXtpSp protein_sp);
   void addPeptideMatch(const PeptideMatch &peptide_match);

src/output/ods/comparspectrasheet.cpp

@@ -110,7 +110,7 @@ ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
                                    const Label *p_label)
 {
   qDebug() << "ComparEmpaiSheet::writeComparValue begin";
-  _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
+  _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun, p_label));
   qDebug() << "ComparEmpaiSheet::writeComparValue end";
 }
 
@@ -130,21 +130,47 @@ ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
 {
   qDebug() << "ComparNsafSheet::writeComparValue begin";
   pappso::pappso_double proto_nsaf_sum = 0;
-  std::pair<std::map<const MsRun *, pappso::pappso_double>::iterator, bool>
-    ret = _map_proto_nsaf_sum_by_msrun.insert(
-      std::pair<const MsRun *, pappso::pappso_double>(p_msrun, 0));
-  if(ret.second == false)
+
+  if(_label_list.size() > 0)
     {
-      //"element 'z' already existed";
-      proto_nsaf_sum = ret.first->second;
+      std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+        _map_proto_nsaf_sum_by_msrun.insert(
+          std::pair<QString, pappso::pappso_double>(
+            QString("%1--%2").arg(p_msrun->getXmlId()).arg(p_label->getXmlId()),
+            0));
+      if(ret.second == false)
+        {
+          //"element 'z' already existed";
+          proto_nsaf_sum = ret.first->second;
+        }
+      else
+        {
+          proto_nsaf_sum = _p_current_identification_group->computeProtoNsafSum(
+            p_msrun, p_label);
+          ret.first->second = proto_nsaf_sum;
+        }
+
+      _p_writer->writeCell(
+        p_protein_match->getNsaf(proto_nsaf_sum, p_msrun, p_label));
     }
   else
     {
-      proto_nsaf_sum =
-        _p_current_identification_group->computeProtoNsafSum(p_msrun);
-      ret.first->second = proto_nsaf_sum;
+      std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+        _map_proto_nsaf_sum_by_msrun.insert(
+          std::pair<QString, pappso::pappso_double>(p_msrun->getXmlId(), 0));
+      if(ret.second == false)
+        {
+          //"element 'z' already existed";
+          proto_nsaf_sum = ret.first->second;
+        }
+      else
+        {
+          proto_nsaf_sum =
+            _p_current_identification_group->computeProtoNsafSum(p_msrun);
+          ret.first->second = proto_nsaf_sum;
+        }
+
+      _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
     }
-
-  _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
   qDebug() << "ComparNsafSheet::writeComparValue end";
 }

src/output/ods/comparspectrasheet.h

@@ -104,7 +104,7 @@ class ComparNsafSheet : public ComparBaseSheet
                                 const Label *p_label = nullptr) override;
 
   private:
-  std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
+  std::map<QString, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
 };
 
 #endif // COMPARSPECTRASHEET_H