WIP: replacing scan number by index

src/core/peptideevidence.cpp

@@ -35,18 +35,20 @@
 
 std::hash<std::string> PeptideEvidence::_hash_fn;
 
-PeptideEvidence::PeptideEvidence(MsRun *msrunid_sp, unsigned int scan)
+PeptideEvidence::PeptideEvidence(MsRun *msrunid_sp, std::size_t scan_index)
 {
-  _msrunid_sp = msrunid_sp;
-  _scan       = scan;
+  _msrunid_sp  = msrunid_sp;
+  m_scan_index = scan_index;
 
-  _hash_sample_scan = PeptideEvidence::_hash_fn(
-    QString("%1 %2").arg(msrunid_sp->getXmlId()).arg(_scan).toStdString());
+  _hash_sample_scan      = PeptideEvidence::_hash_fn(QString("%1 %2")
+                                                  .arg(msrunid_sp->getXmlId())
+                                                  .arg(m_scan_index)
+                                                  .toStdString());
   _identification_engine = IdentificationEngine::unknown;
 }
 
 PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
-  : PeptideEvidence(other._msrunid_sp, other._scan)
+  : PeptideEvidence(other._msrunid_sp, other.m_scan_index)
 {
   _hash_sample_scan        = other._hash_sample_scan;
   _sp_grp_peptide          = other._sp_grp_peptide;
@@ -60,6 +62,8 @@ PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
   _checked                 = other._checked;
   _proxy_valid             = other._proxy_valid;
   _identification_engine   = other._identification_engine;
+  m_scan_index             = other.m_scan_index;
+  m_scan_number            = other.m_scan_number;
 }
 
 pappso::pappso_double
@@ -291,9 +295,9 @@ PeptideEvidence::getIdentificationDataSource() const
   return _p_identification_source;
 }
 unsigned int
-PeptideEvidence::getScan() const
+PeptideEvidence::getScanNumber() const
 {
-  return _scan;
+  return m_scan_number;
 }
 pappso::pappso_double
 PeptideEvidence::getRetentionTime() const

src/core/peptideevidence.h

@@ -49,7 +49,7 @@ typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp;
 class PeptideEvidence
 {
   public:
-  PeptideEvidence(MsRun *msrunid_sp, unsigned int scan);
+  PeptideEvidence(MsRun *msrunid_sp, std::size_t scan_index);
   PeptideEvidence(const PeptideEvidence &other);
   std::size_t getHashSampleScan() const;
   std::size_t getHashPeptideMassSample() const;
@@ -117,7 +117,7 @@ class PeptideEvidence
 
   const MsRun *getMsRunP() const;
   IdentificationDataSource *getIdentificationDataSource() const;
-  unsigned int getScan() const;
+  unsigned int getScanNumber() const;
   pappso::pappso_double getRetentionTime() const;
   unsigned int getCharge() const;
   const PeptideXtpSp &getPeptideXtpSp() const;
@@ -154,7 +154,8 @@ class PeptideEvidence
   private:
   static std::hash<std::string> _hash_fn;
   MsRun *_msrunid_sp;
-  unsigned int _scan = 0;
+  std::size_t m_scan_index  = 0;
+  unsigned int m_scan_number = 0;
   size_t _hash_sample_scan;
   pappso::GrpPeptideSp _sp_grp_peptide;
   PeptideXtpSp _peptide_sp;

src/output/ods/ptm/ptmspectrasheet.cpp

@@ -194,7 +194,7 @@ PtmSpectraSheet::writeBestPeptideEvidence(
     p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
   _p_writer->clearTableCellStyleRef();
   _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
-  _p_writer->writeCell(p_peptide_evidence->getScan());
+  _p_writer->writeCell(p_peptide_evidence->getScanNumber());
   _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
   _p_writer->writeCell(p_peptide_evidence->getCharge());
   _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());

src/output/ods/spectrasheet.cpp

@@ -136,7 +136,7 @@ SpectraSheet::writeBestPeptideEvidence(
     p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
   _p_writer->clearTableCellStyleRef();
   _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
-  _p_writer->writeCell(p_peptide_evidence->getScan());
+  _p_writer->writeCell(p_peptide_evidence->getScanNumber());
   _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
   _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
   _p_writer->writeCell(

win64/home.cmake

@@ -6,9 +6,9 @@ set(ODSSTREAM_QT5_FOUND 1)
 set(ODSSTREAM_INCLUDE_DIR "/home/olivier/eclipse/git/libodsstream/src")
 set(ODSSTREAM_QT5_LIBRARY "/home/olivier/eclipse/git/libodsstream/build/src/libodsstream-qt5.so")
 
-#set(PAPPSOMSPP_QT5_FOUND 1)
-#set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
-#set(PAPPSOMSPP_INCLUDE_DIR "/home/olivier/eclipse/git/pappsomspp/src")
-#set(PAPPSOMSPP_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
-#set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
+set(PAPPSOMSPP_QT5_FOUND 1)
+set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
+set(PAPPSOMSPP_INCLUDE_DIR "/home/olivier/eclipse/git/pappsomspp/src")
+set(PAPPSOMSPP_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
+set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")