Reformat all src files and handle change MsRunStatistics for tdf format

src/core/automaticfilterparameters.h

@@ -51,12 +51,12 @@ class AutomaticFilterParameters
   unsigned int getFilterMinimumPeptidePerMatch() const;
   bool getFilterCrossSamplePeptideNumber() const;
   unsigned int getFilterPeptideObservedInLessSamplesThan() const;
-  
+
   bool useFDR() const;
 
 
   private:
-  double m_filterFDR = -1;
+  double m_filterFDR                                   = -1;
   pappso::pappso_double _filter_minimum_peptide_evalue = 1;
   pappso::pappso_double _filter_minimum_protein_evalue = 1;
   unsigned int _filter_minimum_peptide_per_match       = 1;

src/core/identification_sources/identificationmascotdatfile.cpp

@@ -36,8 +36,8 @@
 
 IdentificationMascotDatFile::IdentificationMascotDatFile(
   const QFileInfo &mascot_dat_file)
-  : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
-  , _mascot_dat_file(mascot_dat_file)
+  : IdentificationDataSource(mascot_dat_file.absoluteFilePath()),
+    _mascot_dat_file(mascot_dat_file)
 {
   _engine = IdentificationEngine::mascot;
 }

src/core/identification_sources/identificationmascotdatfile.h

@@ -51,4 +51,3 @@ class IdentificationMascotDatFile : public IdentificationDataSource
   private:
   const QFileInfo _mascot_dat_file;
 };
-

src/core/msrun.cpp

@@ -52,7 +52,7 @@ MsRun::MsRun(const QString &location) : pappso::MsRunId(location)
 
 MsRun::MsRun(const MsRun &other) : pappso::MsRunId(other)
 {
-  _param_stats = other._param_stats;
+  _param_stats      = other._param_stats;
   m_centroidOptions = other.m_centroidOptions;
 }
 

src/core/peptidextp.h

@@ -58,7 +58,7 @@ class PeptideXtp : public pappso::Peptide
   /** @brief human readable string that contains modifications
    * @param without_label get modifications without existing labels
    * */
-  const QString getModifString(bool without_label =false) const;
+  const QString getModifString(bool without_label = false) const;
 
   /** @brief replace modification in peptide
    */

src/core/proteinxtp.cpp

@@ -185,9 +185,13 @@ class DigestionHandler : public pappso::EnzymeProductInterface
   public:
   void
   setPeptide(std::int8_t sequence_database_id,
-             const pappso::ProteinSp &protein_sp, bool is_decoy,
-             const QString &peptide, unsigned int start, bool is_nter,
-             unsigned int missed_cleavage_number, bool semi_enzyme) override
+             const pappso::ProteinSp &protein_sp,
+             bool is_decoy,
+             const QString &peptide,
+             unsigned int start,
+             bool is_nter,
+             unsigned int missed_cleavage_number,
+             bool semi_enzyme) override
   {
     _peptide_list.append(peptide);
   };
@@ -237,7 +241,7 @@ ProteinXtp::countTrypticPeptidesForPAI() const
 void
 ProteinXtp::parseAccession2dbxref()
 {
-  //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   QStringList access_list = getAccession().split("|");
   // if (access.length == 1)
   QRegExp atg("^[Aa][Tt][MmCc1-5][Gg]\\d{5}\\.?\\d?$");

src/core/qvalue/computeqvalues.cpp

@@ -216,13 +216,14 @@ ComputeQvalues::writeDistributionsByEngines(CalcWriterInterface *p_writer) const
         }
       // double qvalue = Utils::computeFdr(count_decoy, count_target);
       // pep->setParam(PeptideEvidenceParam::pappso_qvalue, QVariant(qvalue));
-      p_writer->writeCell((int) count_target);
+      p_writer->writeCell((int)count_target);
 
-      p_writer->writeCell((int) count_decoy);
+      p_writer->writeCell((int)count_decoy);
 
       p_writer->writeCell(pep->getEvalue());
 
-      p_writer->writeCell(pep->getParam(PeptideEvidenceParam::pappso_qvalue).toDouble());
+      p_writer->writeCell(
+        pep->getParam(PeptideEvidenceParam::pappso_qvalue).toDouble());
       p_writer->writeLine();
     }
 }

src/core/qvalue/computeqvalues.h

@@ -46,8 +46,8 @@ class ComputeQvalues
    * Destructor
    */
   ~ComputeQvalues();
-  
-  void writeDistributionsByEngines(CalcWriterInterface * p_writer) const;
+
+  void writeDistributionsByEngines(CalcWriterInterface *p_writer) const;
 
   private:
   void computeTandemPeptideEvidenceQvalues(
@@ -60,7 +60,6 @@ class ComputeQvalues
 
   private:
   std::set<const PeptideEvidence *> m_falsePeptideEvidenceList;
-  
-    std::vector<PeptideEvidence *> m_tandemPeptideEvidenceList;
-  
+
+  std::vector<PeptideEvidence *> m_tandemPeptideEvidenceList;
 };

src/core/tandem_run/tandembatchprocess.cpp

@@ -375,7 +375,7 @@ TandemBatchProcess::runOne(const QString &mz_file)
       try
         {
 
-          //QProcess::ExitStatus Status = xt_process->exitStatus();
+          // QProcess::ExitStatus Status = xt_process->exitStatus();
 
           const QDateTime dt_begin = QDateTime::currentDateTime();
           QSettings settings;

src/core/tandem_run/tandembatchprocess.h

@@ -35,7 +35,8 @@
 class TandemBatchProcess
 {
   public:
-  TandemBatchProcess(MainWindow *p_main_window, WorkMonitorInterface *p_monitor,
+  TandemBatchProcess(MainWindow *p_main_window,
+                     WorkMonitorInterface *p_monitor,
                      const TandemRunBatch &tandem_run_batch);
   virtual ~TandemBatchProcess();
 

src/core/tandem_run/tandemcondorprocess.cpp

@@ -262,9 +262,8 @@ TandemCondorProcess::run()
                 << " -t "
                 << settings.value("timstof/tmp_dir_path", QDir::tempPath())
                      .toString()
-                << "--tandem" << _tandem_run_batch._tandem_bin_path 
-                << "--centroid" << centroidOption
-                << endl;
+                << "--tandem" << _tandem_run_batch._tandem_bin_path
+                << "--centroid" << centroidOption << endl;
             }
           *p_out << "Queue" << endl;
         }

src/core/tandem_run/tandemparameters.cpp

@@ -266,7 +266,7 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
           (label == "residue, potential modification mass 3") ||
           (label == "residue, potential modification motif 1") ||
           (label == "residue, potential modification motif 2") ||
-          (label == "residue, potential modification motif 3")||
+          (label == "residue, potential modification motif 3") ||
           (label == "spectrum, timstof MS2 centroid parameters"))
     {
       // string

src/grouping/groupinggroup.cpp

@@ -275,7 +275,8 @@ unsigned int
 GroupingGroup::countProteinInSubgroup(unsigned int subgroup_number) const
 {
   return std::count_if(
-    _protein_match_list.begin(), _protein_match_list.end(),
+    _protein_match_list.begin(),
+    _protein_match_list.end(),
     [subgroup_number](const ProteinMatch *p_protein_match) {
       if(p_protein_match->getGrpProteinSp().get()->getSubGroupNumber() ==
          subgroup_number)

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -99,7 +99,8 @@ PtmGroupingExperiment::getPtmIslandList() const
 void
 PtmGroupingExperiment::numbering()
 {
-  std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),
+  std::sort(_ptm_island_group_list.begin(),
+            _ptm_island_group_list.end(),
             [](const PtmIslandGroupSp a, const PtmIslandGroupSp b) {
               return *(a.get()) < *(b.get());
             });
@@ -192,7 +193,8 @@ PtmGroupingExperiment::mergePeptideMatchPtmIslandList(
   for(PtmIslandSp ptm_island_sp : ptm_island_list)
     {
       // http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
-      if(std::none_of(new_ptm_island_list.begin(), new_ptm_island_list.end(),
+      if(std::none_of(new_ptm_island_list.begin(),
+                      new_ptm_island_list.end(),
                       [ptm_island_sp](PtmIslandSp element) {
                         return element.get()->merge(ptm_island_sp);
                       }))

src/grouping/ptm/ptmisland.cpp

@@ -152,7 +152,8 @@ bool
 PtmIsland::containsPeptideMatch(const PeptideMatch &peptide_match) const
 {
 
-  return std::any_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+  return std::any_of(_peptide_match_list.begin(),
+                     _peptide_match_list.end(),
                      [peptide_match](const PeptideMatch &element) {
                        return (peptide_match == element);
                      });
@@ -199,7 +200,8 @@ PtmIsland::getProteinStartPosition() const
 bool
 PtmIsland::merge(PtmIslandSp ptm_island_sp)
 {
-  if(std::none_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+  if(std::none_of(_peptide_match_list.begin(),
+                  _peptide_match_list.end(),
                   [ptm_island_sp](const PeptideMatch &element) {
                     return ptm_island_sp.get()->containsPeptideMatch(element);
                   }))
@@ -213,7 +215,8 @@ PtmIsland::merge(PtmIslandSp ptm_island_sp)
         _peptide_match_list.begin(),
         ptm_island_sp.get()->_peptide_match_list.begin(),
         ptm_island_sp.get()->_peptide_match_list.end());
-      std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+      std::sort(_peptide_match_list.begin(),
+                _peptide_match_list.end(),
                 [](const PeptideMatch &a, const PeptideMatch &b) {
                   return (a.operator<(b));
                 });
@@ -231,14 +234,16 @@ PtmIsland::merge(PtmIslandSp ptm_island_sp)
 
 
       std::vector<PeptideMatch>::const_iterator it_result =
-        std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+        std::max_element(_peptide_match_list.begin(),
+                         _peptide_match_list.end(),
                          [](const PeptideMatch &a, const PeptideMatch &b) {
                            return (a.getStop() < b.getStop());
                          });
       _protein_stop = it_result->getStop();
 
       it_result =
-        std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+        std::min_element(_peptide_match_list.begin(),
+                         _peptide_match_list.end(),
                          [](const PeptideMatch &a, const PeptideMatch &b) {
                            return a.getStart() < b.getStart();
                          });

src/grouping/ptm/ptmislandgroup.cpp

@@ -80,7 +80,8 @@ PtmIslandGroup::setGroupNumber(unsigned int number)
     {
       ptm_island_subgroup.get()->setPtmIslandGroup(this);
     }
-  std::sort(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+  std::sort(_ptm_island_subgroup_list.begin(),
+            _ptm_island_subgroup_list.end(),
             [](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
               return (a.get()->getFirstPtmIsland()->getProteinStartPosition() <
                       b.get()->getFirstPtmIsland()->getProteinStartPosition());
@@ -116,7 +117,8 @@ unsigned int
 PtmIslandGroup::maxCountSampleScan() const
 {
   std::vector<PtmIslandSubgroupSp>::const_iterator it_result = std::max_element(
-    _ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+    _ptm_island_subgroup_list.begin(),
+    _ptm_island_subgroup_list.end(),
     [](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
       return (a.get()->countSampleScan() < b.get()->countSampleScan());
     });

src/grouping/ptm/ptmislandsubgroup.cpp

@@ -73,7 +73,8 @@ PtmIslandSubgroup::setSubgroupNumber(unsigned int number)
       ptm_island.get()->setPtmIslandSubgroup(this);
     }
   std::sort(
-    _ptm_island_list.begin(), _ptm_island_list.end(),
+    _ptm_island_list.begin(),
+    _ptm_island_list.end(),
     [](const PtmIslandSp &a, const PtmIslandSp &b) {
       return (
         a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <
@@ -92,7 +93,8 @@ PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup *p_ptm_island_group)
 {
   _ptm_island_group_p = p_ptm_island_group;
   std::sort(
-    _ptm_island_list.begin(), _ptm_island_list.end(),
+    _ptm_island_list.begin(),
+    _ptm_island_list.end(),
     [](const PtmIslandSp &a, const PtmIslandSp &b) {
       return (
         a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <

src/grouping/ptm/ptmsamplescan.cpp

@@ -95,7 +95,8 @@ PtmSampleScan::add(const PeptideMatch &peptide_match)
   // qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
 
   // sort list
-  std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+  std::sort(_peptide_match_list.begin(),
+            _peptide_match_list.end(),
             [](const PeptideMatch &first, const PeptideMatch &second) {
               return (first.getPeptideEvidence()->getEvalue() <
                       second.getPeptideEvidence()->getEvalue());

src/gui/about_dialog/aboutdialog.h

@@ -30,7 +30,7 @@
 
 namespace Ui
 {
-  class AboutDialog;
+class AboutDialog;
 }
 
 class AboutDialog : public QDialog

src/gui/choose_modification_dialog/choosemodificationdialog.cpp

@@ -48,17 +48,25 @@ ChooseModificationDialog::ChooseModificationDialog(QWidget *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(ui->modification_listview, &QListView::clicked, this,
+  connect(ui->modification_listview,
+          &QListView::clicked,
+          this,
           &ChooseModificationDialog::ItemClicked);
-  connect(ui->modification_listview, &QListView::doubleClicked, this,
+  connect(ui->modification_listview,
+          &QListView::doubleClicked,
+          this,
           &ChooseModificationDialog::ItemDoubleClicked);
 #else
   // Qt4 code
 
-  connect(ui->modification_listview, SIGNAL(clicked(const QModelIndex)), this,
+  connect(ui->modification_listview,
+          SIGNAL(clicked(const QModelIndex)),
+          this,
           SLOT(ItemClicked(QModelIndex)));
-  connect(ui->modification_listview, SIGNAL(doubleClicked(const QModelIndex)),
-          this, SLOT(ItemDoubleClicked(QModelIndex)));
+  connect(ui->modification_listview,
+          SIGNAL(doubleClicked(const QModelIndex)),
+          this,
+          SLOT(ItemDoubleClicked(QModelIndex)));
 
 #endif
 }