diff --git a/src/core/identification_sources/identificationmascotdatfile.cpp b/src/core/identification_sources/identificationmascotdatfile.cpp
index aacb8ea517eb62c0c760931366bca8dc865abf2a..2115e67551f49c958ac6527cb2ed56c4fcd0d4fe 100644
--- a/src/core/identification_sources/identificationmascotdatfile.cpp
+++ b/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;
 }
diff --git a/src/core/identification_sources/identificationpepxmlfile.cpp b/src/core/identification_sources/identificationpepxmlfile.cpp
index 563aea5cb05a6df53e6909cacbc5c7d4705801cc..636cca993f32f539cfad1cc7217d4f68c02e8253 100644
--- a/src/core/identification_sources/identificationpepxmlfile.cpp
+++ b/src/core/identification_sources/identificationpepxmlfile.cpp
@@ -33,8 +33,8 @@
 
 IdentificationPepXmlFile::IdentificationPepXmlFile(
   const QFileInfo &mascot_dat_file)
-  : IdentificationDataSource(mascot_dat_file.absoluteFilePath()),
-    _pep_xml_file(mascot_dat_file)
+  : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
+  , _pep_xml_file(mascot_dat_file)
 {
   _engine = IdentificationEngine::unknown;
 }
diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index e86cdda76bd5d2c1b70849595340cba181bc4c14..809e1f758220cc3571619becd4b2649dea7c4e74 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -34,8 +34,8 @@
 #include <pappsomspp/pappsoexception.h>
 
 IdentificationPwizFile::IdentificationPwizFile(const QFileInfo &ident_file)
-  : IdentificationDataSource(ident_file.absoluteFilePath()),
-    _ident_file(ident_file)
+  : IdentificationDataSource(ident_file.absoluteFilePath())
+  , _ident_file(ident_file)
 {
   //_engine = IdentificationEngine::XTandem;
   _engine = IdentificationEngine::peptider;
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index adc0ce5564be8ee613c3c94cab38f3f085a668d9..33d45f996146214defce0e050e4c7b2995098cc8 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -28,8 +28,8 @@
 
 IdentificationXtandemFile::IdentificationXtandemFile(
   const QFileInfo &xtandem_file)
-  : IdentificationDataSource(xtandem_file.absoluteFilePath()),
-    _xtandem_file(xtandem_file)
+  : IdentificationDataSource(xtandem_file.absoluteFilePath())
+  , _xtandem_file(xtandem_file)
 {
   _engine = IdentificationEngine::XTandem;
 }
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index e668b13ef473d230e538ce5598dbd468390d2bd2..853af05959f50367ca10f2f8fab835d840200ee2 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -130,8 +130,7 @@ 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))
@@ -209,8 +208,7 @@ 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)
                            {
@@ -303,8 +301,8 @@ 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);
@@ -354,8 +352,7 @@ 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;
@@ -478,9 +475,7 @@ 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;
@@ -489,8 +484,8 @@ 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);
         }
     }
 }
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index f723d8b7f901b4861a1f0626b5245fb3b2a0cf8f..398f85bc5ec38df3a1efb42526359fdf92811580 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -160,8 +160,7 @@ 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
@@ -172,8 +171,7 @@ 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:
diff --git a/src/core/labeling/label.cpp b/src/core/labeling/label.cpp
index 85b8963994897acd639f436aee47f2801da6e676..39743bc7c8b5c33d21ec33ab8dd6dbf4dd55b534 100644
--- a/src/core/labeling/label.cpp
+++ b/src/core/labeling/label.cpp
@@ -85,8 +85,7 @@ Label::containsAaModificationP(
 {
   for(LabelModification label_modification : _modification_list)
     {
-      if(std::find(modification_set.begin(),
-                   modification_set.end(),
+      if(std::find(modification_set.begin(), modification_set.end(),
                    label_modification.modification) != modification_set.end())
         {
           return true;
diff --git a/src/core/peptidextp.cpp b/src/core/peptidextp.cpp
index 7330913b0883b79f2245ff4c6beed5bd328a3d1a..1d5db480d153b1ad9300b63a1a2d06d3607444ad 100644
--- a/src/core/peptidextp.cpp
+++ b/src/core/peptidextp.cpp
@@ -121,8 +121,8 @@ PeptideXtp::applyLabelingMethod(LabelingMethodSp labeling_method_sp)
     {
       std::list<pappso::AaModificationP> aa_modif_list =
         amino_acid.getModificationList();
-      modification_set.insert(
-        modification_set.begin(), aa_modif_list.begin(), aa_modif_list.end());
+      modification_set.insert(modification_set.begin(), aa_modif_list.begin(),
+                              aa_modif_list.end());
     }
   modification_set.unique();
 
diff --git a/src/core/project.cpp b/src/core/project.cpp
index fb5ee702aa1b0901d5e33451f124a56b3811663c..effd7a3af2d0ea19870b51d08fbbfbc0ffee3cad 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -281,13 +281,11 @@ Project::hasPtmExperiment() const
 void
 Project::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
 {
   for(const IdentificationGroup *p_ident_group : _identification_goup_list)
     {
-      p_ident_group->getSameXicPeptideEvidenceList(
-        peptide_evidence_list, p_msrun, p_peptide, charge);
+      p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
+                                                   p_msrun, p_peptide, charge);
     }
 }
diff --git a/src/core/project.h b/src/core/project.h
index 6db5c633b6a566665d53018d2f0e2526dd1730b7..3fbbdd7ae6dadb78b96b14a3408423b6662f9515 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -98,8 +98,7 @@ class Project
    */
   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:
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 700dedd321de85960ea1f91b585aa68343a54d89..42ff60b176f8c29fb1d0516b1a83251fcda0a7e7 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -282,8 +282,7 @@ ProteinMatch::getPeptideMatchList(ValidationState state,
 }
 
 unsigned int
-ProteinMatch::countSampleScan(ValidationState state,
-                              const MsRun *p_msrun_id,
+ProteinMatch::countSampleScan(ValidationState state, const MsRun *p_msrun_id,
                               const Label *p_label) const
 {
   std::vector<std::size_t> count_sample_scan;
@@ -330,8 +329,7 @@ unsigned int
 ProteinMatch::countPeptideMatch(ValidationState state) const
 {
   return std::count_if(
-    _peptide_match_list.begin(),
-    _peptide_match_list.end(),
+    _peptide_match_list.begin(), _peptide_match_list.end(),
     [state](const PeptideMatch &peptide_match) {
       if(peptide_match.getPeptideEvidence()->getValidationState() >= state)
         {
@@ -345,8 +343,7 @@ ProteinMatch::countPeptideMatch(ValidationState state) const
 }
 
 size_t
-ProteinMatch::countSequenceLi(ValidationState state,
-                              const MsRun *p_msrun_id,
+ProteinMatch::countSequenceLi(ValidationState state, const MsRun *p_msrun_id,
                               const Label *p_label) const
 {
   // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -561,8 +558,7 @@ 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 Label *p_label) const
+                      const MsRun *p_msrun_id, const Label *p_label) const
 {
   if(proto_nsaf_sum == 0)
     {
@@ -585,8 +581,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id, const Label *p_label) const
             QObject::tr("protein has no amino acid sequence"));
         }
       pappso::pappso_double proto_nsaf =
-        (pappso::pappso_double)countSampleScan(
-          ValidationState::validAndChecked, sp_msrun_id, p_label) /
+        (pappso::pappso_double)countSampleScan(ValidationState::validAndChecked,
+                                               sp_msrun_id, p_label) /
         (pappso::pappso_double)_protein_sp.get()->size();
       return proto_nsaf;
     }
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index c46f92ebba40063be3b1e8c4eb009cc35e6f4334..ce76f6abc8aa5a05c1c6ff95cef72b56745bf373 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -185,13 +185,9 @@ 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);
   };
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index dbd7ca8f0cd7daeb408eda4879dae9c77ba5ae1b..0c1029745885e06a449f13565567f6beb1f04769 100644
--- a/src/core/tandem_run/tandembatchprocess.h
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -35,8 +35,7 @@
 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();
 
diff --git a/src/core/tandem_run/tandemcondorprocess.cpp b/src/core/tandem_run/tandemcondorprocess.cpp
index f05d317dbac15f1ed33f33824d314f5c05331c27..3b5639f99dd8751a3ed8d5cdeb8e595f86dadb9f 100644
--- a/src/core/tandem_run/tandemcondorprocess.cpp
+++ b/src/core/tandem_run/tandemcondorprocess.cpp
@@ -634,9 +634,8 @@ TandemCondorProcess::setCondorJobStatus(std::int8_t count_status[10])
 {
 
   QString status_message =
-    QString(
-      "%1 unexpanded jobs\n%2 idle jobs\n%3 running jobs\n%4 removed "
-      "jobs\n%5 completed jobs\n%6 held jobs\n%7 submission errors")
+    QString("%1 unexpanded jobs\n%2 idle jobs\n%3 running jobs\n%4 removed "
+            "jobs\n%5 completed jobs\n%6 held jobs\n%7 submission errors")
       .arg(count_status[0])
       .arg(count_status[1])
       .arg(count_status[2])
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index cfcf224ee59c3d41676855090b3e470296d71863..f86ef82f9760c374ed06e7641064a5e44f0a273a 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -275,8 +275,7 @@ 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)
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index d2d75064d66e2756be7f952cc6f0f39e2f4ed691..4e8e373f268855aa82cf2f3ef404773ba455e65c 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -113,8 +113,7 @@ GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp,
 {
 
   return _p_grp_experiment->setGrpPeptide(
-    proteinSp,
-    p_peptide_evidence->getPeptideXtpSp().get()->getSequence(),
+    proteinSp, p_peptide_evidence->getPeptideXtpSp().get()->getSequence(),
     p_peptide_evidence->getPeptideXtpSp().get()->getGroupingMass());
 }
 
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index dc25f640cb9feda6321d4284696fdee553de2c2b..903b26226f25877255e61e8dca6a0689fc306817 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -99,8 +99,7 @@ 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());
             });
@@ -193,8 +192,7 @@ 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);
                       }))
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 17cc60d32efac94a1ef1b27d41b9af1a2ab2ca92..98c15f4a205e5caceccdb4c6a74da173cfb071b3 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -152,8 +152,7 @@ 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);
                      });
@@ -200,8 +199,7 @@ 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);
                   }))
@@ -215,8 +213,7 @@ 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));
                 });
@@ -234,16 +231,14 @@ 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();
                          });
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index ca793c67f86b0039aeb8590bfe9a9ba161ba60cf..0f3a2b3843cc90cc434e0dba4634b5a567ba7e09 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/src/grouping/ptm/ptmislandgroup.cpp
@@ -80,8 +80,7 @@ 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());
@@ -117,8 +116,7 @@ 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());
     });
diff --git a/src/grouping/ptm/ptmislandsubgroup.cpp b/src/grouping/ptm/ptmislandsubgroup.cpp
index 7a5c334e4be5dd377bf2eb7d13bce429056f434a..d43c016a88b6ab81de3aa763192dfd0517f50d6f 100644
--- a/src/grouping/ptm/ptmislandsubgroup.cpp
+++ b/src/grouping/ptm/ptmislandsubgroup.cpp
@@ -73,8 +73,7 @@ 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() <
@@ -93,8 +92,7 @@ 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() <
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 3837399f20a4b9d18ae10a00ac93fb26d4850d1b..623eb6d9d4560d27fa637695c9394ef8f0afef56 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -95,8 +95,7 @@ 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());
diff --git a/src/gui/about_dialog/aboutdialog.h b/src/gui/about_dialog/aboutdialog.h
index 260a0435210534fadee1a3c392c51097502d4e8f..fe2b90f2b675fff928daa1702965bd0c42070983 100644
--- a/src/gui/about_dialog/aboutdialog.h
+++ b/src/gui/about_dialog/aboutdialog.h
@@ -30,7 +30,7 @@
 
 namespace Ui
 {
-class AboutDialog;
+  class AboutDialog;
 }
 
 class AboutDialog : public QDialog
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
index 1a9fd625658a77ae0815b30e09b009d82cca5551..e1d4d90a849d19cb5039226081ce5dc28849a556 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
@@ -48,25 +48,17 @@ 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
 }
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.h b/src/gui/choose_modification_dialog/choosemodificationdialog.h
index c641196ff83e978e3505103e76dd3d348cee0270..2b5e42b25bdc0ebc58793b5687d833be06717148 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.h
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.h
@@ -33,7 +33,7 @@
 
 namespace Ui
 {
-class ChooseModificationDialog;
+  class ChooseModificationDialog;
 }
 
 class ChooseModificationDialog : public QDialog
diff --git a/src/gui/edit_label_methods/editlabelmethods.cpp b/src/gui/edit_label_methods/editlabelmethods.cpp
index b965d07c958cf477553ce14705111c690cda80a8..738841833d8f7b7c7494483a8d518feb7d11eaed 100644
--- a/src/gui/edit_label_methods/editlabelmethods.cpp
+++ b/src/gui/edit_label_methods/editlabelmethods.cpp
@@ -40,15 +40,11 @@ EditLabelMethods::EditLabelMethods(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(ui->method_list_view,
-          &QListView::clicked,
-          this,
+  connect(ui->method_list_view, &QListView::clicked, this,
           &EditLabelMethods::ItemClicked);
 #else
 
-  connect(ui->method_list_view,
-          SIGNAL(clicked(const QModelIndex)),
-          this,
+  connect(ui->method_list_view, SIGNAL(clicked(const QModelIndex)), this,
           SLOT(ItemClicked(QModelIndex)));
 
 
@@ -74,15 +70,15 @@ EditLabelMethods::setProjectSp(ProjectSp project_sp)
   if(!xml_doc.open(QIODevice::ReadOnly))
     {
       // error
-      QMessageBox::warning(
-        this, tr("error"), tr("error opening catalog_label resource file"));
+      QMessageBox::warning(this, tr("error"),
+                           tr("error opening catalog_label resource file"));
       return;
     }
   if(!dom->setContent(&xml_doc))
     {
       xml_doc.close();
-      QMessageBox::warning(
-        this, tr("error"), tr("error setting catalog_label xml content"));
+      QMessageBox::warning(this, tr("error"),
+                           tr("error setting catalog_label xml content"));
       return;
     }
 
diff --git a/src/gui/edit_label_methods/editlabelmethods.h b/src/gui/edit_label_methods/editlabelmethods.h
index 4bfb8a5f05ec7af1c0e62e1b8ef551175b5057e9..5b05b7b325c514f396a79c1603452bc418be570d 100644
--- a/src/gui/edit_label_methods/editlabelmethods.h
+++ b/src/gui/edit_label_methods/editlabelmethods.h
@@ -35,7 +35,7 @@ class ProjectWindow;
 
 namespace Ui
 {
-class EditLabelMethodView;
+  class EditLabelMethodView;
 }
 
 class EditLabelMethods : public QDialog
diff --git a/src/gui/edit_modifications/editmodifications.cpp b/src/gui/edit_modifications/editmodifications.cpp
index f5064ff99670bfe2f0e5049faa5bd68787ec25fd..a71a751f48c6d3b83fecaf78d1c2555cd7cdd0cc 100644
--- a/src/gui/edit_modifications/editmodifications.cpp
+++ b/src/gui/edit_modifications/editmodifications.cpp
@@ -42,33 +42,21 @@ EditModifications::EditModifications(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(ui->modification_list_view,
-          &QListView::clicked,
-          this,
+  connect(ui->modification_list_view, &QListView::clicked, this,
           &EditModifications::ItemClicked);
-  connect(ui->modification_list_view,
-          &QListView::doubleClicked,
-          this,
+  connect(ui->modification_list_view, &QListView::doubleClicked, this,
           &EditModifications::ItemDoubleClicked);
 
-  connect(_p_browse_modification_dialog,
-          &ChooseModificationDialog::accepted,
-          this,
-          &EditModifications::doAcceptedBrowseDialog);
+  connect(_p_browse_modification_dialog, &ChooseModificationDialog::accepted,
+          this, &EditModifications::doAcceptedBrowseDialog);
 #else
 
-  connect(ui->modification_list_view,
-          SIGNAL(clicked(const QModelIndex)),
-          this,
+  connect(ui->modification_list_view, SIGNAL(clicked(const QModelIndex)), this,
           SLOT(ItemClicked(QModelIndex)));
-  connect(ui->modification_list_view,
-          SIGNAL(doubleClicked(const QModelIndex)),
-          this,
-          SLOT(ItemDoubleClicked(QModelIndex)));
-
-  connect(_p_browse_modification_dialog,
-          SIGNAL(accepted()),
-          this,
+  connect(ui->modification_list_view, SIGNAL(doubleClicked(const QModelIndex)),
+          this, SLOT(ItemDoubleClicked(QModelIndex)));
+
+  connect(_p_browse_modification_dialog, SIGNAL(accepted()), this,
           SLOT(doAcceptedBrowseDialog()));
 
 #endif
diff --git a/src/gui/edit_modifications/editmodifications.h b/src/gui/edit_modifications/editmodifications.h
index 3758ea3f244aec5bdcf3cc2fcfa4030c27d58213..36f0b1416084fd06e2dccb8ff6e9f6bf422ae184 100644
--- a/src/gui/edit_modifications/editmodifications.h
+++ b/src/gui/edit_modifications/editmodifications.h
@@ -36,7 +36,7 @@ class ProjectWindow;
 // http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui
 {
-class EditModificationView;
+  class EditModificationView;
 }
 
 class EditModifications : public QMainWindow
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index 2ef02ef4168830d12459528e940d578686eceeaa..598e3a75e03ff1c4e45a102b80b2e05921915988 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -140,8 +140,7 @@ EditTandemPresetDialog::doSelectDir()
   catch(pappso::PappsoException &error)
     {
       QMessageBox::warning(
-        this,
-        tr("Error :"),
+        this, tr("Error :"),
         tr("Error choosing preset directory : %1").arg(error.qwhat()));
     }
 }
@@ -188,8 +187,7 @@ EditTandemPresetDialog::doLoad()
       else
         {
           QMessageBox::warning(
-            this,
-            tr("Error :"),
+            this, tr("Error :"),
             tr("%1 is not an X!Tandem parameter file")
               .arg(p_tandem_preset_file->getAbsoluteFilePath()));
         }
@@ -1292,8 +1290,7 @@ EditTandemPresetDialog::done(int r)
       if(!_p_tandem_preset_file->exists())
         {
           QMessageBox::warning(
-            this,
-            tr("Save parameters"),
+            this, tr("Save parameters"),
             tr("Parameters file does not exists.\nPlease save it before "
                "pressing ok or cancel edition"));
           return;
@@ -1308,8 +1305,7 @@ EditTandemPresetDialog::done(int r)
       else
         {
           QMessageBox::warning(
-            this,
-            tr("Save parameters"),
+            this, tr("Save parameters"),
             tr("Parameters modified but not saved.\nPlease save it before "
                "pressing ok or cancel edition"));
           return;
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
index 871142793c070ea30e867e5fafd12d33e1710d0e..fffcef16775658a557d0f997f20e5605de315601 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
@@ -36,7 +36,7 @@
 
 namespace Ui
 {
-class EditTandemPresetView;
+  class EditTandemPresetView;
 }
 
 class EditTandemPresetDialog : public QDialog
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index d79c0fe93db59e37ced2cfdf9d29ca570c2f2db1..fe8c70493c8eb672cc70adfe32057573c35c2ca2 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -36,7 +36,7 @@
 
 namespace Ui
 {
-class ExportMasschroqDialog;
+  class ExportMasschroqDialog;
 }
 
 class ExportMasschroqDialog : public QDialog
diff --git a/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h b/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
index d13ee34e2dbda892c624a806bc461d54232404a0..a7302007a2a71c5b6e7912b32ce45df2ae10ebda 100644
--- a/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
+++ b/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
@@ -39,7 +39,7 @@
 
 namespace Ui
 {
-class ExportSpreadsheetDialog;
+  class ExportSpreadsheetDialog;
 }
 
 class ExportSpreadsheetDialog : public QDialog
diff --git a/src/gui/load_results_dialog/loadresultsdialog.cpp b/src/gui/load_results_dialog/loadresultsdialog.cpp
index 8e9d1f8fe5aa9b045bcf5241472db9b07de3d358..058e0d4429690c33caec2c8c50b9098ce565136a 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.cpp
+++ b/src/gui/load_results_dialog/loadresultsdialog.cpp
@@ -104,9 +104,7 @@ LoadResultsDialog::chooseFiles()
         settings.value("path/identificationfiles", "").toString();
 
       QStringList filenames = QFileDialog::getOpenFileNames(
-        this,
-        tr("identification files"),
-        default_location,
+        this, tr("identification files"), default_location,
         tr(
           "X!Tandem, Mascot DAT, pepXML or mzIdentML files (*.xml *.mzid *.dat "
           "*.pepxml *.pepXML);;all files (*)"));
diff --git a/src/gui/load_results_dialog/loadresultsdialog.h b/src/gui/load_results_dialog/loadresultsdialog.h
index 6ba44e428100e6f2623bc8daef725dda77b79e40..613e058c2f3d273e1a51cb210692da82f4b2660e 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.h
+++ b/src/gui/load_results_dialog/loadresultsdialog.h
@@ -33,7 +33,7 @@
 
 namespace Ui
 {
-class LoadResultsDialog;
+  class LoadResultsDialog;
 }
 
 
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index e05fd6a2ae2a8a3f3acd46b58629c45ed226524b..adef989239291b214d67ec9c63cc3f4b05285b08 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -73,36 +73,22 @@ MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_p_tandem_run_dialog,
-          &TandemRunDialog::accepted,
-          this,
+  connect(_p_tandem_run_dialog, &TandemRunDialog::accepted, this,
           &MainWindow::doAcceptedTandemRunDialog);
-  connect(_p_load_results_dialog,
-          &LoadResultsDialog::accepted,
-          this,
+  connect(_p_load_results_dialog, &LoadResultsDialog::accepted, this,
           &MainWindow::doAcceptedLoadResultDialog);
-  connect(_p_export_spreadsheet_dialog,
-          &ExportSpreadsheetDialog::accepted,
-          this,
-          &MainWindow::doAcceptedExportSpreadsheetDialog);
-  connect(&m_onlineVersion,
-          &HttpVersion::httpVersionReady,
-          this,
+  connect(_p_export_spreadsheet_dialog, &ExportSpreadsheetDialog::accepted,
+          this, &MainWindow::doAcceptedExportSpreadsheetDialog);
+  connect(&m_onlineVersion, &HttpVersion::httpVersionReady, this,
           &MainWindow::doCheckNewVersion);
 #else
   // Qt4 code
 
-  connect(_p_tandem_run_dialog,
-          SIGNAL(accepted()),
-          this,
+  connect(_p_tandem_run_dialog, SIGNAL(accepted()), this,
           SLOT(doAcceptedTandemRunDialog()));
-  connect(_p_load_results_dialog,
-          SIGNAL(accepted()),
-          this,
+  connect(_p_load_results_dialog, SIGNAL(accepted()), this,
           SLOT(doAcceptedLoadResultDialog()));
-  connect(_p_export_spreadsheet_dialog,
-          SIGNAL(accepted()),
-          this,
+  connect(_p_export_spreadsheet_dialog, SIGNAL(accepted()), this,
           SLOT(doAcceptedExportSpreadsheetDialog()));
 
 #endif
@@ -210,8 +196,7 @@ MainWindow::doAcceptedExportSpreadsheetDialog()
       if(format == "ods")
         {
           filename = QFileDialog::getSaveFileName(
-            this,
-            tr("Save ODS file"),
+            this, tr("Save ODS file"),
             QString("%1/untitled.ods").arg(default_location),
             tr("Open Document Spreadsheet (*.ods)"));
 
@@ -392,11 +377,9 @@ MainWindow::selectXpipFile()
       QSettings settings;
       QString default_location = settings.value("path/xpipfile", "").toString();
 
-      QString filename =
-        QFileDialog::getOpenFileName(this,
-                                     tr("Open XPIP File"),
-                                     default_location,
-                                     tr("xpip files (*.xpip);;all files (*)"));
+      QString filename = QFileDialog::getOpenFileName(
+        this, tr("Open XPIP File"), default_location,
+        tr("xpip files (*.xpip);;all files (*)"));
 
       if(filename.isEmpty())
         {
@@ -428,10 +411,8 @@ MainWindow::doActionSaveProject()
 
 
       QString filename = QFileDialog::getSaveFileName(
-        this,
-        tr("Save XPIP file"),
-        QString("%1/untitled.xpip").arg(default_location),
-        tr("XPIP (*.xpip)"));
+        this, tr("Save XPIP file"),
+        QString("%1/untitled.xpip").arg(default_location), tr("XPIP (*.xpip)"));
 
       if(filename.isEmpty())
         {
@@ -479,10 +460,8 @@ MainWindow::doActionSpectralCountingMcq()
   QString default_location = settings.value("path/scmcqfile", "").toString();
 
   QString filename = QFileDialog::getSaveFileName(
-    this,
-    tr("Save spectral count TSV file"),
-    QString("%1/untitled.tsv").arg(default_location),
-    tr("TSV (*.tsv)"));
+    this, tr("Save spectral count TSV file"),
+    QString("%1/untitled.tsv").arg(default_location), tr("TSV (*.tsv)"));
 
   if(filename.isEmpty())
     {
@@ -504,10 +483,8 @@ MainWindow::doActionFasta()
   QString default_location = settings.value("path/fastafile", "").toString();
 
   QString filename = QFileDialog::getSaveFileName(
-    this,
-    tr("Save FASTA file"),
-    QString("%1/untitled.fasta").arg(default_location),
-    tr("FASTA (*.fasta)"));
+    this, tr("Save FASTA file"),
+    QString("%1/untitled.fasta").arg(default_location), tr("FASTA (*.fasta)"));
 
   if(filename.isEmpty())
     {
@@ -529,10 +506,8 @@ MainWindow::doActionFastaOneBySubgroup()
   QString default_location = settings.value("path/fastafile", "").toString();
 
   QString filename = QFileDialog::getSaveFileName(
-    this,
-    tr("Save FASTA file"),
-    QString("%1/untitled.fasta").arg(default_location),
-    tr("FASTA (*.fasta)"));
+    this, tr("Save FASTA file"),
+    QString("%1/untitled.fasta").arg(default_location), tr("FASTA (*.fasta)"));
 
   if(filename.isEmpty())
     {
@@ -543,8 +518,8 @@ MainWindow::doActionFastaOneBySubgroup()
 
   showWaitingMessage(
     tr("Writing %1 FASTA file").arg(QFileInfo(filename).fileName()));
-  emit operateWritingFastaFile(
-    filename, _project_sp, ExportFastaType::oneBySubgroup);
+  emit operateWritingFastaFile(filename, _project_sp,
+                               ExportFastaType::oneBySubgroup);
 }
 
 void
@@ -554,10 +529,8 @@ MainWindow::doActionFastaOneByGroup()
   QString default_location = settings.value("path/fastafile", "").toString();
 
   QString filename = QFileDialog::getSaveFileName(
-    this,
-    tr("Save FASTA file"),
-    QString("%1/untitled.fasta").arg(default_location),
-    tr("FASTA (*.fasta)"));
+    this, tr("Save FASTA file"),
+    QString("%1/untitled.fasta").arg(default_location), tr("FASTA (*.fasta)"));
 
   if(filename.isEmpty())
     {
@@ -568,8 +541,8 @@ MainWindow::doActionFastaOneByGroup()
 
   showWaitingMessage(
     tr("Writing %1 FASTA file").arg(QFileInfo(filename).fileName()));
-  emit operateWritingFastaFile(
-    filename, _project_sp, ExportFastaType::oneByGroup);
+  emit operateWritingFastaFile(filename, _project_sp,
+                               ExportFastaType::oneByGroup);
 }
 
 void
@@ -583,10 +556,8 @@ MainWindow::doActionMassChroQ()
       if(_p_export_masschroq_dialog == nullptr)
         {
           _p_export_masschroq_dialog = new ExportMasschroqDialog(this);
-          connect(_p_export_masschroq_dialog,
-                  &ExportMasschroqDialog::accepted,
-                  this,
-                  &MainWindow::doAcceptedExportMasschroqDialog);
+          connect(_p_export_masschroq_dialog, &ExportMasschroqDialog::accepted,
+                  this, &MainWindow::doAcceptedExportMasschroqDialog);
         }
 
       MasschroqFileParameters params;
@@ -622,8 +593,7 @@ MainWindow::doAcceptedExportMasschroqDialog()
       QString default_location = settings.value("path/mcqfile", "").toString();
 
       QString filename = QFileDialog::getSaveFileName(
-        this,
-        tr("Save MassChroqML file"),
+        this, tr("Save MassChroqML file"),
         QString("%1/untitled.masschroqml").arg(default_location),
         tr("MassChroqML (*.masschroqml)"));
 
@@ -660,8 +630,7 @@ MainWindow::doActionMassChroqPRM()
         settings.value("path/mcqprmfile", "").toString();
 
       QString filename = QFileDialog::getSaveFileName(
-        this,
-        tr("Save MassChroqPRM file"),
+        this, tr("Save MassChroqPRM file"),
         QString("%1/untitled.masschroqprm").arg(default_location),
         tr("MassChroqPRM (*.masschroqprm)"));
 
@@ -698,8 +667,7 @@ MainWindow::doActionProticDb()
         settings.value("path/proticfile", "").toString();
 
       QString filename = QFileDialog::getSaveFileName(
-        this,
-        tr("Save PROTICdbML file"),
+        this, tr("Save PROTICdbML file"),
         QString("%1/untitled.proticdbml").arg(default_location),
         tr("PROTICdbML (*.proticdbml)"));
 
@@ -747,8 +715,7 @@ MainWindow::doCheckNewVersion()
 
       hideWaitingMessage();
       int ret = QMessageBox::warning(
-        this,
-        tr("new version available"),
+        this, tr("new version available"),
         tr("A new %1 version is available %2\nCheck our web site \n"
            "http://pappso.inra.fr/bioinfo/xtandempipeline\n to download it")
           .arg(SOFTWARE_NAME)
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index e55123a45d07d047243f5f2b81dc05af784399a7..1371ab2f9ca4ccc76bf14c490104a3bd1b7315f8 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -46,7 +46,7 @@
 
 namespace Ui
 {
-class Main;
+  class Main;
 }
 
 class MainWindow : public QMainWindow
@@ -106,17 +106,15 @@ class MainWindow : public QMainWindow
                              AutomaticFilterParameters param,
                              QStringList file_list);
   void operateWritingXpipFile(QString filename, ProjectSp project_sp);
-  void
-  operateWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
-  void operateWritingMassChroqFile(QString filename,
-                                   ProjectSp project_sp,
+  void operateWritingOdsFile(QString filename, QString format,
+                             ProjectSp project_sp);
+  void operateWritingMassChroqFile(QString filename, ProjectSp project_sp,
                                    MasschroqFileParameters params);
   void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
   void operateWritingProticFile(QString filename, ProjectSp project_sp);
   void operateWritingMcqrSpectralCountFile(QString filename,
                                            ProjectSp project_sp);
-  void operateWritingFastaFile(QString filename,
-                               ProjectSp project_sp,
+  void operateWritingFastaFile(QString filename, ProjectSp project_sp,
                                ExportFastaType type);
   void operateGrouping(ProjectSp project_sp);
   void operateRunningXtandem(TandemRunBatch tandem_run_batch);
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 4172be076aa686267835ed0f82e90ef26596eee3..e39f2d675b84a8157294005b158a9d190c41049c 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -113,18 +113,12 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_p_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &PeptideWindow::doIdentificationGroupGrouped);
 
-  connect(this,
-          &PeptideWindow::loadSpectrumSp,
-          worker,
+  connect(this, &PeptideWindow::loadSpectrumSp, worker,
           &SpectrumSpLoaderThread::doLoadSpectrumSp);
-  connect(worker,
-          &SpectrumSpLoaderThread::spectrumSpReady,
-          this,
+  connect(worker, &SpectrumSpLoaderThread::spectrumSpReady, this,
           &PeptideWindow::doSpectrumSpReady);
 
   /*
@@ -146,20 +140,15 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
 #else
   // Qt4 code
   connect(_p_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
 
-  connect(this,
-          SIGNAL(loadSpectrumSp(PeptideMatch *)),
-          worker,
+  connect(this, SIGNAL(loadSpectrumSp(PeptideMatch *)), worker,
           SLOT(doLoadSpectrumSp(PeptideMatch *)));
-  connect(worker,
-          SIGNAL(spectrumSpReady(pappso::SpectrumSp, QString, QString)),
-          this,
-          SLOT(doSpectrumSpReady(pappso::SpectrumSp, QString, QString)));
-  connect(
-    _p_spectrum_overlay, SIGNAL(mzChanged(double)), this, SLOT(setMz(double)));
+  connect(worker, SIGNAL(spectrumSpReady(pappso::SpectrumSp, QString, QString)),
+          this, SLOT(doSpectrumSpReady(pappso::SpectrumSp, QString, QString)));
+  connect(_p_spectrum_overlay, SIGNAL(mzChanged(double)), this,
+          SLOT(setMz(double)));
   // connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
   // SLOT(updateStatusBar()));
 #endif
@@ -257,8 +246,7 @@ PeptideWindow::updateDisplay()
       ui->mz_label->setText(
         QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(
                           _p_peptide_evidence->getCharge()),
-                        'f',
-                        4));
+                        'f', 4));
       ui->expmz_label->setText(
         QString::number(_p_peptide_evidence->getExperimentalMz(), 'f', 4));
       ui->delta_label->setText(
@@ -270,14 +258,13 @@ PeptideWindow::updateDisplay()
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      QMessageBox::warning(this,
-                           tr("Unable to display peptide details :"),
+      QMessageBox::warning(this, tr("Unable to display peptide details :"),
                            exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
     {
-      QMessageBox::warning(
-        this, tr("Unable to display peptide details :"), exception_std.what());
+      QMessageBox::warning(this, tr("Unable to display peptide details :"),
+                           exception_std.what());
     }
 }
 
@@ -288,11 +275,9 @@ PeptideWindow::chooseDefaultMzDataDir()
   QSettings settings;
   QString default_location = settings.value("path/mzdatadir", "").toString();
 
-  QString filename =
-    QFileDialog::getExistingDirectory(this,
-                                      tr("Choose default mz data directory"),
-                                      default_location,
-                                      QFileDialog::ShowDirsOnly);
+  QString filename = QFileDialog::getExistingDirectory(
+    this, tr("Choose default mz data directory"), default_location,
+    QFileDialog::ShowDirsOnly);
 
   if(filename.isEmpty())
     {
@@ -339,8 +324,7 @@ PeptideWindow::openInXicViewer()
 
 void
 PeptideWindow::doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
-                                 QString error,
-                                 QString fatal_error)
+                                 QString error, QString fatal_error)
 {
   qDebug() << "PeptideWindow::doSpectrumSpReady begin error=" << error
            << " fatal_error=" << fatal_error;
@@ -379,8 +363,7 @@ PeptideWindow::doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
       // fatal_error
 
       QMessageBox::warning(
-        this,
-        tr("Oops! an error occurred in XTPCPP. Dont Panic :"),
+        this, tr("Oops! an error occurred in XTPCPP. Dont Panic :"),
         fatal_error);
       ui->statusbar->showMessage(tr("ERROR reading spectrum"));
       QSettings settings;
@@ -469,11 +452,9 @@ PeptideWindow::doSaveSvg()
               .arg(_p_peptide_evidence->getScan());
         }
 
-      QString filename =
-        QFileDialog::getSaveFileName(this,
-                                     tr("Save SVG file"),
-                                     proposed_filename,
-                                     tr("Scalable Vector Graphic (*.svg)"));
+      QString filename = QFileDialog::getSaveFileName(
+        this, tr("Save SVG file"), proposed_filename,
+        tr("Scalable Vector Graphic (*.svg)"));
 
       if(filename.isEmpty())
         {
@@ -484,10 +465,8 @@ PeptideWindow::doSaveSvg()
 
 
       ui->spectrum_widget->toSvgFile(
-        filename,
-        tr("%1 SVG spectrum generator").arg(SOFTWARE_NAME),
-        tr("This is an annotated SVG spectrum"),
-        QSize(1200, 500));
+        filename, tr("%1 SVG spectrum generator").arg(SOFTWARE_NAME),
+        tr("This is an annotated SVG spectrum"), QSize(1200, 500));
       // emit operateXpipFile(filename);
     }
   catch(pappso::PappsoException &error)
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index f5629040a752435ef419ba97fe748be01299cb90..dd02efa5ee7769acbf66a80c42574e5845c29103 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -37,7 +37,7 @@ class ProjectWindow;
 
 namespace Ui
 {
-class PeptideDetailView;
+  class PeptideDetailView;
 }
 
 
@@ -49,8 +49,7 @@ class SpectrumSpLoaderThread : public QObject
   void doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence);
 
   signals:
-  void spectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
-                       QString error,
+  void spectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp, QString error,
                        QString fatal_error);
 
   protected:
@@ -78,8 +77,7 @@ class PeptideWindow : public QMainWindow
   void loadSpectrumSp(PeptideEvidence *p_peptide_evidence);
 
   protected slots:
-  void doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
-                         QString error,
+  void doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp, QString error,
                          QString fatal_error);
   void doMsmsPrecisionChanged(pappso::PrecisionPtr);
   void doSaveSvg();
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index f3cd586a0cd114589733f2b0575b58b216500896..533afa4a0925949a48bb0450421cf06ef6c31a62 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -47,9 +47,7 @@ PeptideListQactionColumn::PeptideListQactionColumn(PeptideListWindow *parent,
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(this,
-          &PeptideListQactionColumn::toggled,
-          this,
+  connect(this, &PeptideListQactionColumn::toggled, this,
           &PeptideListQactionColumn::doToggled);
 #else
   // Qt4 code
@@ -121,47 +119,30 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &PeptideListWindow::doIdentificationGroupGrouped);
 
-  connect(this,
-          &PeptideListWindow::peptideDataChanged,
-          _peptide_table_model_p,
+  connect(this, &PeptideListWindow::peptideDataChanged, _peptide_table_model_p,
           &PeptideTableModel::onPeptideDataChanged);
 
-  connect(ui->tableView,
-          &QTableView::clicked,
-          _p_proxy_model,
+  connect(ui->tableView, &QTableView::clicked, _p_proxy_model,
           &PeptideTableProxyModel::onTableClicked);
-  connect(_peptide_table_model_p,
-          &PeptideTableModel::layoutChanged,
-          this,
+  connect(_peptide_table_model_p, &PeptideTableModel::layoutChanged, this,
           &PeptideListWindow::updateStatusBar);
-  connect(ui->centralwidget,
-          &QWidget::customContextMenuRequested,
-          this,
+  connect(ui->centralwidget, &QWidget::customContextMenuRequested, this,
           &PeptideListWindow::showContextMenu);
 #else
   // Qt4 code
   connect(_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
 
-  connect(this,
-          SIGNAL(peptideDataChanged()),
-          _peptide_table_model_p,
+  connect(this, SIGNAL(peptideDataChanged()), _peptide_table_model_p,
           SLOT(onPeptideDataChanged()));
 
-  connect(ui->tableView,
-          SIGNAL(clicked(const QModelIndex &)),
-          _p_proxy_model,
+  connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model,
           SLOT(onTableClicked(const QModelIndex &)));
-  connect(_peptide_table_model_p,
-          SIGNAL(layoutChanged()),
-          this,
+  connect(_peptide_table_model_p, SIGNAL(layoutChanged()), this,
           SLOT(updateStatusBar()));
 
   /*
diff --git a/src/gui/peptide_list_view/peptidelistwindow.h b/src/gui/peptide_list_view/peptidelistwindow.h
index ffea46d7a7e6418eb7c5a2a059171f6f8f5365fa..3aecc924345bfec4835131df1c3699bc8b8041c7 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.h
+++ b/src/gui/peptide_list_view/peptidelistwindow.h
@@ -36,7 +36,7 @@ class ProjectWindow;
 // http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui
 {
-class PeptideView;
+  class PeptideView;
 }
 
 
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index efe5c63f6cea2e3a0d61bef8cd983edf3e4993e0..b8ed59b4a8e15fa27f029f7f44259040a31baf43 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -152,8 +152,7 @@ PeptideTableModel::columnCount(const QModelIndex &parent) const
   return 40;
 }
 QVariant
-PeptideTableModel::headerData(int section,
-                              Qt::Orientation orientation,
+PeptideTableModel::headerData(int section, Qt::Orientation orientation,
                               int role) const
 {
   if(orientation == Qt::Horizontal)
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index eeee8485fe104c2d4daf8384c8ba50c3c9a3a5cc..82addadd8757bfac6d28c98547af3114c3eef8ee 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -88,8 +88,8 @@ class PeptideTableModel : public QAbstractTableModel
   PeptideTableModel(PeptideListWindow *parent);
   int rowCount(const QModelIndex &parent = QModelIndex()) const override;
   int columnCount(const QModelIndex &parent = QModelIndex()) const override;
-  QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  QVariant headerData(int section, Qt::Orientation orientation,
+                      int role) const override;
   QVariant data(const QModelIndex &index,
                 int role = Qt::DisplayRole) const override;
 
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 3c0ec4d7c5a3069fb5a0c1da80346c775e37748f..3993cd41216919b5d97d242828271b8d9e6a68f6 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -317,8 +317,7 @@ PeptideTableProxyModel::lessThan(const QModelIndex &left,
 
 
 QVariant
-PeptideTableProxyModel::headerData(int section,
-                                   Qt::Orientation orientation,
+PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
                                    int role) const
 {
   int col = mapToSource(index(0, section)).column();
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.h b/src/gui/peptide_list_view/peptidetableproxymodel.h
index 123ce4b4f71c0cd4ea9c98bb9ff6a14153bad3f6..569bc20165262113be3f1f742115c9b48e215375 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.h
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.h
@@ -47,8 +47,8 @@ class PeptideTableProxyModel : public QSortFilterProxyModel
   bool filterAcceptsColumn(int source_column,
                            const QModelIndex &source_parent) const override;
 
-  QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  QVariant headerData(int section, Qt::Orientation orientation,
+                      int role) const override;
   QVariant data(const QModelIndex &index,
                 int role = Qt::DisplayRole) const override;
   bool lessThan(const QModelIndex &left,
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index d95594793e536d60d89d6ba96f9ae1dc88578a6d..bea55aeb5e5e1773a59c884ebe21fb6933fdac95 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -52,16 +52,13 @@ IdentificationGroupWidget::setIdentificationGroup(
   _p_project_window = parent;
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_p_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &IdentificationGroupWidget::doIdentificationGroupGrouped);
 #else
   // Qt4 code
 
   connect(_p_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
 #endif
 }
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
index 0e34d4b4d4be6d6f033da400ae08aa60dfca592a..94d03b4be10e66674a09776ee399a786e35ef7af 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
@@ -29,7 +29,7 @@
 
 namespace Ui
 {
-class IdentificationGroupWidget;
+  class IdentificationGroupWidget;
 }
 
 
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index b4422aa6cc8c6a1902451cefa157fea50b0c4859..a0f8424471c70a95ac2ac315e0125a714e2d4330 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -84,21 +84,14 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
 #if QT_VERSION >= 0x050000
   // Qt5 code
   connect(ui->filter_parameter_widget,
-          &AutomaticFilterWidget::automaticFilterParametersChanged,
-          this,
+          &AutomaticFilterWidget::automaticFilterParametersChanged, this,
           &ProjectWindow::doAutomaticFilterParametersChanged);
-  connect(ui->contaminant_widget,
-          &ContaminantWidget::changed,
-          this,
+  connect(ui->contaminant_widget, &ContaminantWidget::changed, this,
           &ProjectWindow::doContaminantSelectionChanged);
-  connect(ui->decoy_widget,
-          &DecoyWidget::changed,
-          this,
+  connect(ui->decoy_widget, &DecoyWidget::changed, this,
           &ProjectWindow::doDecoySelectionChanged);
 
-  connect(_p_edit_label_methods,
-          &EditLabelMethods::accepted,
-          this,
+  connect(_p_edit_label_methods, &EditLabelMethods::accepted, this,
           &ProjectWindow::doAcceptedLabelingMethod);
 
 #else
@@ -110,9 +103,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
           this,
           SLOT(doAutomaticFilterParametersChanged(AutomaticFilterParameters)));
 
-  connect(_p_edit_label_methods,
-          SIGNAL(accepted()),
-          this,
+  connect(_p_edit_label_methods, SIGNAL(accepted()), this,
           SLOT(doAcceptedLabelingMethod()));
 
   // connect(this, SIGNAL(operateGrouping(ProjectSp)),
@@ -221,13 +212,13 @@ ProjectWindow::refreshPtmGroup(IdentificationGroup *p_ident_group)
         }
       catch(pappso::PappsoException exception_pappso)
         {
-          QMessageBox::warning(
-            this, tr("Unable to display project :"), exception_pappso.qwhat());
+          QMessageBox::warning(this, tr("Unable to display project :"),
+                               exception_pappso.qwhat());
         }
       catch(std::exception exception_std)
         {
-          QMessageBox::warning(
-            this, tr("Unable to display project :"), exception_std.what());
+          QMessageBox::warning(this, tr("Unable to display project :"),
+                               exception_std.what());
         }
     }
   qDebug() << "ProjectWindow::refreshPtmGroup end";
@@ -249,13 +240,13 @@ ProjectWindow::refreshGroup(IdentificationGroup *p_ident_group)
         }
       catch(pappso::PappsoException exception_pappso)
         {
-          QMessageBox::warning(
-            this, tr("Unable to display project :"), exception_pappso.qwhat());
+          QMessageBox::warning(this, tr("Unable to display project :"),
+                               exception_pappso.qwhat());
         }
       catch(std::exception exception_std)
         {
-          QMessageBox::warning(
-            this, tr("Unable to display project :"), exception_std.what());
+          QMessageBox::warning(this, tr("Unable to display project :"),
+                               exception_std.what());
         }
     }
   qDebug() << "ProjectWindow::refreshGroup end";
@@ -295,13 +286,13 @@ ProjectWindow::computeFdr()
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      QMessageBox::warning(
-        this, tr("Unable to compute FDR :"), exception_pappso.qwhat());
+      QMessageBox::warning(this, tr("Unable to compute FDR :"),
+                           exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
     {
-      QMessageBox::warning(
-        this, tr("Unable to compute FDR :"), exception_std.what());
+      QMessageBox::warning(this, tr("Unable to compute FDR :"),
+                           exception_std.what());
     }
   qDebug() << "ProjectWindow::computeFdr end";
 }
@@ -386,8 +377,7 @@ ProjectWindow::computeMassPrecision()
       ui->mass_precision_mean_label->setText("0");
       ui->mass_precision_median_label->setText("0");
       ui->mass_precision_sd_label->setText("0");
-      QMessageBox::warning(this,
-                           tr("Unable to compute mass precision :"),
+      QMessageBox::warning(this, tr("Unable to compute mass precision :"),
                            exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
@@ -395,8 +385,8 @@ ProjectWindow::computeMassPrecision()
       ui->mass_precision_mean_label->setText("0");
       ui->mass_precision_median_label->setText("0");
       ui->mass_precision_sd_label->setText("0");
-      QMessageBox::warning(
-        this, tr("Unable to compute mass precision :"), exception_std.what());
+      QMessageBox::warning(this, tr("Unable to compute mass precision :"),
+                           exception_std.what());
     }
   qDebug() << "ProjectWindow::computeMassPrecision end";
 }
@@ -912,14 +902,14 @@ ProjectWindow::doApplyDecoy()
   catch(pappso::PappsoException exception_pappso)
     {
       hideWaitingMessage();
-      QMessageBox::warning(
-        this, tr("Error filtering results :"), exception_pappso.qwhat());
+      QMessageBox::warning(this, tr("Error filtering results :"),
+                           exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
     {
       hideWaitingMessage();
-      QMessageBox::warning(
-        this, tr("Error filtering results :"), exception_std.what());
+      QMessageBox::warning(this, tr("Error filtering results :"),
+                           exception_std.what());
     }
 }
 
@@ -946,13 +936,13 @@ ProjectWindow::doApplyFilter()
   catch(pappso::PappsoException exception_pappso)
     {
       hideWaitingMessage();
-      QMessageBox::warning(
-        this, tr("Error filtering results :"), exception_pappso.qwhat());
+      QMessageBox::warning(this, tr("Error filtering results :"),
+                           exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
     {
       hideWaitingMessage();
-      QMessageBox::warning(
-        this, tr("Error filtering results :"), exception_std.what());
+      QMessageBox::warning(this, tr("Error filtering results :"),
+                           exception_std.what());
     }
 }
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 836e4d3da83ab4c494a8bb491bcb564b0082af9b..c625843da2b451d42e7a31a8860bafdf240190db 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -42,7 +42,7 @@ class MainWindow;
 // http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui
 {
-class ProjectView;
+  class ProjectView;
 }
 
 class ProjectWindow : public QMainWindow
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 4a05e8cfc67ee48de0a6447eca2af04bc744e7b2..73648355426d11880bc79d9f6c6fcf09d939c753 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -47,9 +47,7 @@ ProteinListQactionColumn::ProteinListQactionColumn(ProteinListWindow *parent,
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(this,
-          &ProteinListQactionColumn::toggled,
-          this,
+  connect(this, &ProteinListQactionColumn::toggled, this,
           &ProteinListQactionColumn::doToggled);
 #else
   // Qt4 code
@@ -118,41 +116,26 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &ProteinListWindow::doIdentificationGroupGrouped);
 
-  connect(this,
-          &ProteinListWindow::proteinDataChanged,
-          _protein_table_model_p,
+  connect(this, &ProteinListWindow::proteinDataChanged, _protein_table_model_p,
           &ProteinTableModel::onProteinDataChanged);
-  connect(ui->tableView,
-          &QTableView::clicked,
-          _p_proxy_model,
+  connect(ui->tableView, &QTableView::clicked, _p_proxy_model,
           &ProteinTableProxyModel::onTableClicked);
-  connect(ui->centralwidget,
-          &QWidget::customContextMenuRequested,
-          this,
+  connect(ui->centralwidget, &QWidget::customContextMenuRequested, this,
           &ProteinListWindow::showContextMenu);
-  connect(_protein_table_model_p,
-          &ProteinTableModel::layoutChanged,
-          this,
+  connect(_protein_table_model_p, &ProteinTableModel::layoutChanged, this,
           &ProteinListWindow::updateStatusBar);
 #else
   // Qt4 code
   connect(_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
 
-  connect(this,
-          SIGNAL(proteinDataChanged()),
-          _protein_table_model_p,
+  connect(this, SIGNAL(proteinDataChanged()), _protein_table_model_p,
           SLOT(onProteinDataChanged()));
-  connect(ui->tableView,
-          SIGNAL(clicked(const QModelIndex &)),
-          _p_proxy_model,
+  connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model,
           SLOT(onTableClicked(const QModelIndex &)));
   // connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)),
   // _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
@@ -162,15 +145,11 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
 
   // connect( this, SIGNAL( focusReceived(bool) ),this,
   // SLOT(doFocusReceived(bool)) );
-  connect(ui->centralwidget,
-          SIGNAL(customContextMenuRequested(const QPoint &)),
-          this,
-          SLOT(showContextMenu(const QPoint &)));
+  connect(ui->centralwidget, SIGNAL(customContextMenuRequested(const QPoint &)),
+          this, SLOT(showContextMenu(const QPoint &)));
   // connect(_p_proxy_model, SIGNAL(layoutChanged()),
   //        this, SLOT(doProxyLayoutChanged()));
-  connect(_protein_table_model_p,
-          SIGNAL(layoutChanged()),
-          this,
+  connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
           SLOT(updateStatusBar()));
 #endif
 }
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index b7ed2a105c1966a192fe0b388c2e740d691ad87d..a1015a9a3cb4dae50f4d6ba401aacd6fc6ad002b 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -37,7 +37,7 @@ class ProjectWindow;
 // http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui
 {
-class ProteinView;
+  class ProteinView;
 }
 
 class ProteinListWindow;
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index cbe0d4ec5f2a45efc88689b8402ea446fc9c957c..490f40bb9af62e4406a2325e0be34d837bfa13f1 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -209,8 +209,7 @@ ProteinTableModel::getDescription(std::int8_t column)
   return "";
 }
 QVariant
-ProteinTableModel::headerData(int section,
-                              Qt::Orientation orientation,
+ProteinTableModel::headerData(int section, Qt::Orientation orientation,
                               int role) const
 {
   if(_p_identification_group == nullptr)
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index 86734bcf813dc4a1fda284133f18ae3b4022908a..6cdaa1ce25844a2f4998f71d9d9dcc886edb3b90 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -62,8 +62,8 @@ class ProteinTableModel : public QAbstractTableModel
   rowCount(const QModelIndex &parent = QModelIndex()) const override;
   virtual int
   columnCount(const QModelIndex &parent = QModelIndex()) const override;
-  virtual QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  virtual QVariant headerData(int section, Qt::Orientation orientation,
+                              int role) const override;
   virtual QVariant data(const QModelIndex &index,
                         int role = Qt::DisplayRole) const override;
 
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index 336061c75e591b40f9e15cfb9d996e6cd18486c8..2db9e8aefd9c6201009b2deed12f2e57c81e2fe2 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -378,8 +378,7 @@ ProteinTableProxyModel::data(const QModelIndex &index, int role) const
 }
 
 QVariant
-ProteinTableProxyModel::headerData(int section,
-                                   Qt::Orientation orientation,
+ProteinTableProxyModel::headerData(int section, Qt::Orientation orientation,
                                    int role) const
 {
   int col = mapToSource(index(0, section)).column();
diff --git a/src/gui/protein_list_view/proteintableproxymodel.h b/src/gui/protein_list_view/proteintableproxymodel.h
index d4f6877009bef5cb49ad67d901df975fa9b38be2..adefbcb080a05dd1168a1d9e1232a685c7adb328 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.h
+++ b/src/gui/protein_list_view/proteintableproxymodel.h
@@ -48,8 +48,8 @@ class ProteinTableProxyModel : public QSortFilterProxyModel
   bool filterAcceptsColumn(int source_column,
                            const QModelIndex &source_parent) const override;
 
-  QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  QVariant headerData(int section, Qt::Orientation orientation,
+                      int role) const override;
   QVariant data(const QModelIndex &index,
                 int role = Qt::DisplayRole) const override;
   bool lessThan(const QModelIndex &left,
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 9b17a774131f682d834fc69f17021a984c3ae7ee..397c5aea1d13b5147743012ce162e161b06a970a 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -39,8 +39,8 @@ DbXrefButton::DbXrefButton(QWidget *parent, DbXref dbxref) : QPushButton(parent)
   _dbxref = dbxref;
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  QObject::connect(
-    this, &DbXrefButton::clicked, this, &DbXrefButton::clickedSlot);
+  QObject::connect(this, &DbXrefButton::clicked, this,
+                   &DbXrefButton::clickedSlot);
 #else
   // Qt4 code
   QObject::connect(this, SIGNAL(clicked()), this, SLOT(clickedSlot()));
@@ -67,23 +67,16 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_p_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &ProteinWindow::doIdentificationGroupGrouped);
-  connect(_p_project_window,
-          &ProjectWindow::peptideEvidenceSelected,
-          this,
+  connect(_p_project_window, &ProjectWindow::peptideEvidenceSelected, this,
           &ProteinWindow::doPeptideEvidenceSelected);
 #else
   // Qt4 code
   connect(_p_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-  connect(_p_project_window,
-          SIGNAL(peptideMatchSelected(PeptideMatch *)),
-          this,
+  connect(_p_project_window, SIGNAL(peptideMatchSelected(PeptideMatch *)), this,
           SLOT(doPeptideMatchSelected(PeptideMatch *)));
 
   // connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
@@ -150,10 +143,9 @@ ProteinWindow::updateDisplay()
           _p_protein_match->getProteinXtpSp().get()->getDbxrefList())
         {
           QString accession = ui->accession_label->text().replace(
-            dbxref.accession,
-            QString("<span style=\"color:%2;\">%1</span>")
-              .arg(dbxref.accession)
-              .arg("blue"));
+            dbxref.accession, QString("<span style=\"color:%2;\">%1</span>")
+                                .arg(dbxref.accession)
+                                .arg("blue"));
           ui->accession_label->setText(accession);
           qDebug() << "ProteinWindow::updateDisplay " << accession;
 
@@ -179,14 +171,13 @@ ProteinWindow::updateDisplay()
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      QMessageBox::warning(this,
-                           tr("Unable to display protein details :"),
+      QMessageBox::warning(this, tr("Unable to display protein details :"),
                            exception_pappso.qwhat());
     }
   catch(std::exception exception_std)
     {
-      QMessageBox::warning(
-        this, tr("Unable to display protein details :"), exception_std.what());
+      QMessageBox::warning(this, tr("Unable to display protein details :"),
+                           exception_std.what());
     }
 }
 
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index 1e2885b4f4142fda6da638c1adaa54abb5130677..8bb6fcf33d8d49ce293db8ed755a560169e8409b 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -46,7 +46,7 @@ class ProjectWindow;
 
 namespace Ui
 {
-class ProteinDetailView;
+  class ProteinDetailView;
 }
 
 class ProteinWindow : public QMainWindow
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 880533bae6ba0fb865d6f9704aa69cc4d68110cf..5114d8f0d6450f6ebcad0c3d370d3c34f0e6af36 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -63,46 +63,30 @@ PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(this,
-          &PtmIslandListWindow::ptmIslandDataChanged,
-          _ptm_table_model_p,
+  connect(this, &PtmIslandListWindow::ptmIslandDataChanged, _ptm_table_model_p,
           &PtmIslandTableModel::onPtmIslandDataChanged);
 
-  connect(_project_window,
-          &ProjectWindow::identificationPtmGroupGrouped,
-          this,
+  connect(_project_window, &ProjectWindow::identificationPtmGroupGrouped, this,
           &PtmIslandListWindow::doIdentificationPtmGroupGrouped);
-  connect(_project_window,
-          &ProjectWindow::identificationGroupGrouped,
-          this,
+  connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
           &PtmIslandListWindow::doIdentificationGroupGrouped);
-  connect(ui->ptm_island_tableview,
-          &QTableView::clicked,
-          _ptm_proxy_model_p,
+  connect(ui->ptm_island_tableview, &QTableView::clicked, _ptm_proxy_model_p,
           &PtmIslandProxyModel::onTableClicked);
-  connect(_ptm_table_model_p,
-          &PtmIslandTableModel::layoutChanged,
-          this,
+  connect(_ptm_table_model_p, &PtmIslandTableModel::layoutChanged, this,
           &PtmIslandListWindow::updateStatusBar);
 #else
   // Qt4 code
-  connect(this,
-          SIGNAL(ptmIslandDataChanged()),
-          _ptm_table_model_p,
+  connect(this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p,
           SLOT(onPtmIslandDataChanged()));
 
   connect(_project_window,
-          SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
   connect(_project_window,
-          SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
-          this,
+          SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
           SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-  connect(ui->ptm_island_tableview,
-          SIGNAL(clicked(const QModelIndex &)),
-          _ptm_proxy_model_p,
-          SLOT(onTableClicked(const QModelIndex &)));
+  connect(ui->ptm_island_tableview, SIGNAL(clicked(const QModelIndex &)),
+          _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
 
 #endif
 }
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index e5f49d377f648a53de01181f83308767ad0203ca..70cb8e16864ed226b8bd6f18e014e76351cec23c 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -42,7 +42,7 @@ class PtmPeptideListWindow;
 // http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui
 {
-class PtmIslandListWindow;
+  class PtmIslandListWindow;
 }
 
 class PtmIslandListWindow : public QMainWindow
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 9057339b4609e74b2b55246ac43768cc8861bda7..d039db1fe402edff4d6d9ff8fcea4b678fba7991 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -178,8 +178,7 @@ PtmIslandTableModel::columnCount(const QModelIndex &parent) const
   return 0;
 }
 QVariant
-PtmIslandTableModel::headerData(int section,
-                                Qt::Orientation orientation,
+PtmIslandTableModel::headerData(int section, Qt::Orientation orientation,
                                 int role) const
 {
   if(getPtmGroupingExperiment() == nullptr)
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index da20d0d4ad2383fea2d4f1c4d4af2f325e897c21..2cee9bc6260f1f14c7bd0a7ab96649de8104208e 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -70,8 +70,8 @@ class PtmIslandTableModel : public QAbstractTableModel
   rowCount(const QModelIndex &parent = QModelIndex()) const override;
   virtual int
   columnCount(const QModelIndex &parent = QModelIndex()) const override;
-  virtual QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  virtual QVariant headerData(int section, Qt::Orientation orientation,
+                              int role) const override;
   virtual QVariant data(const QModelIndex &index,
                         int role = Qt::DisplayRole) const override;
 
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index da29d92673639291b23af9779cd22c823dd58d18..5fb53774e830b6371d6d0ae1b92aac3e810e5d8a 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -62,12 +62,9 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(ui->ptm_peptide_tableview,
-          &QTableView::clicked,
-          _ptm_proxy_model_p,
+  connect(ui->ptm_peptide_tableview, &QTableView::clicked, _ptm_proxy_model_p,
           &PtmPeptideTableProxyModel::onTableClicked);
-  connect(this,
-          &PtmPeptideListWindow::requestPeptideDetailView,
+  connect(this, &PtmPeptideListWindow::requestPeptideDetailView,
           _p_ptm_island_list_window->getProjectWindowP(),
           &ProjectWindow::doViewPeptideDetail);
 #else
@@ -80,12 +77,9 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
   // this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *))); connect
   // (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup
   // *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-  connect(ui->ptm_peptide_tableview,
-          SIGNAL(clicked(const QModelIndex &)),
-          _ptm_proxy_model_p,
-          SLOT(onTableClicked(const QModelIndex &)));
-  connect(this,
-          SIGNAL(requestPeptideDetailView(PeptideMatch *)),
+  connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)),
+          _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
+  connect(this, SIGNAL(requestPeptideDetailView(PeptideMatch *)),
           _p_ptm_island_list_window->getProjectWindowP(),
           SLOT(doViewPeptideDetail(PeptideMatch *)));
 
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index b4bcc15c85df99bace9e68394e114e486390abe4..d49489ef74f2197e0e22c0dca384ecd5e8b6046c 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -40,7 +40,7 @@ class PtmIslandListWindow;
 
 namespace Ui
 {
-class PtmPeptideListWindow;
+  class PtmPeptideListWindow;
 }
 
 
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 2f9fbd0e2d790f053f130040c61a4f1783a48086..ca333c6a2eb8909b7351cb914800d21ba344f689 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -188,8 +188,7 @@ PtmPeptideTableModel::columnCount(const QModelIndex &parent) const
   return 15;
 }
 QVariant
-PtmPeptideTableModel::headerData(int section,
-                                 Qt::Orientation orientation,
+PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation,
                                  int role) const
 {
   if(orientation == Qt::Horizontal)
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
index 59ae2434804153b5a49fa749f55a2109ace9bee6..76c02ce65b2f5ac008d2fe0dbb74427e876171c1 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
@@ -71,8 +71,8 @@ class PtmPeptideTableModel : public QAbstractTableModel
   rowCount(const QModelIndex &parent = QModelIndex()) const override;
   virtual int
   columnCount(const QModelIndex &parent = QModelIndex()) const override;
-  virtual QVariant
-  headerData(int section, Qt::Orientation orientation, int role) const override;
+  virtual QVariant headerData(int section, Qt::Orientation orientation,
+                              int role) const override;
   virtual QVariant data(const QModelIndex &index,
                         int role = Qt::DisplayRole) const override;
   static const QString getTitle(PtmPeptideListColumn column);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index e370564136dc0eccf7208453cdff35adb2401e18..4a15cc5482239dab46574bb158344a958be9bf97 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -35,8 +35,7 @@
 
 PtmPeptideMenuQicon::PtmPeptideMenuQicon(
   const PtmGroupingExperiment *p_ptm_grouping_experiment,
-  const PtmSampleScan *p_ptm_sample,
-  const PeptideMatch *p_peptide_match)
+  const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match)
   : QIcon(), _peptide_match(*p_peptide_match)
 {
   _p_ptm_sample_scan         = p_ptm_sample;
@@ -46,10 +45,8 @@ PtmPeptideMenuQicon::~PtmPeptideMenuQicon()
 {
 }
 void
-PtmPeptideMenuQicon::paint(QPainter *painter,
-                           const QRect &rect,
-                           Qt::Alignment alignment,
-                           Mode mode,
+PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect,
+                           Qt::Alignment alignment, Mode mode,
                            State state) const
 {
 
@@ -72,15 +69,14 @@ PtmPeptideMenuQicon::paint(QPainter *painter,
 PtmPeptideMenuQaction::PtmPeptideMenuQaction(
   PtmPeptideTableProxyModel *parent,
   const PtmGroupingExperiment *p_ptm_grouping_experiment,
-  const PtmSampleScan *p_ptm_sample,
-  PeptideMatch *p_peptide_match)
+  const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match)
   : QAction(parent)
 {
 
   _p_ptm_peptide_table_proxy_model = parent;
   _peptide_match                   = *p_peptide_match;
-  this->setIcon(PtmPeptideMenuQicon(
-    p_ptm_grouping_experiment, p_ptm_sample, p_peptide_match));
+  this->setIcon(PtmPeptideMenuQicon(p_ptm_grouping_experiment, p_ptm_sample,
+                                    p_peptide_match));
   // this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
 
   QStringList position_list;
@@ -101,9 +97,7 @@ PtmPeptideMenuQaction::PtmPeptideMenuQaction(
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(this,
-          &PtmPeptideMenuQaction::triggered,
-          this,
+  connect(this, &PtmPeptideMenuQaction::triggered, this,
           &PtmPeptideMenuQaction::doTriggered);
 #else
   // Qt4 code
@@ -193,10 +187,8 @@ PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index)
   for(auto p_peptide_match : sp_ptm_sample_scan.get()->getPeptideMatchList())
     {
       p_action = new PtmPeptideMenuQaction(
-        this,
-        _p_ptm_table_model->getPtmGroupingExperiment(),
-        sp_ptm_sample_scan.get(),
-        &p_peptide_match);
+        this, _p_ptm_table_model->getPtmGroupingExperiment(),
+        sp_ptm_sample_scan.get(), &p_peptide_match);
       _p_context_menu->addAction(p_action);
     }
 
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index fc1211eccfbb6a56297d0c021d1035a2e711e8b8..3b458883bfd391828b05e20202daed9b4270f104 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -46,15 +46,12 @@ class PtmPeptideMenuQicon : public QIcon
   public:
   explicit PtmPeptideMenuQicon(
     const PtmGroupingExperiment *p_ptm_grouping_experiment,
-    const PtmSampleScan *p_ptm_sample,
-    const PeptideMatch *p_peptide_match);
+    const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match);
   ~PtmPeptideMenuQicon();
 
-  void paint(QPainter *painter,
-             const QRect &rect,
-             Qt::Alignment alignment = Qt::AlignCenter,
-             Mode mode               = Normal,
-             State state             = Off) const;
+  void paint(QPainter *painter, const QRect &rect,
+             Qt::Alignment alignment = Qt::AlignCenter, Mode mode = Normal,
+             State state = Off) const;
 
   private:
   const PtmSampleScan *_p_ptm_sample_scan;
@@ -69,8 +66,7 @@ class PtmPeptideMenuQaction : public QAction
   explicit PtmPeptideMenuQaction(
     PtmPeptideTableProxyModel *parent,
     const PtmGroupingExperiment *p_ptm_grouping_experiment,
-    const PtmSampleScan *p_ptm_sample,
-    PeptideMatch *p_peptide_match);
+    const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match);
   ~PtmPeptideMenuQaction();
 
   public slots:
diff --git a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
index fef38bde8479a3fe0861ad335932e9ca63d6806e..e9b786bcc63c4700a6db961e0def62f88408155d 100644
--- a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
+++ b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
@@ -41,8 +41,7 @@ class PtmSequenceDelegate : public QStyledItemDelegate
   PtmSequenceDelegate(PtmIslandListWindow *p_ptm_island_list_window,
                       QWidget *parent = 0);
 
-  void paint(QPainter *painter,
-             const QStyleOptionViewItem &option,
+  void paint(QPainter *painter, const QStyleOptionViewItem &option,
              const QModelIndex &index) const override;
   // QSize sizeHint(const QStyleOptionViewItem &option,
   //              const QModelIndex &index) const override;
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 596819d180573beb21a3dbb208eab02c6c96742e..679de92a2959dad3f50130b2488170a2cc58fef9 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -243,13 +243,9 @@ TandemRunDialog::editPresets()
 
 #if QT_VERSION >= 0x050000
   // Qt5 code
-  connect(_p_preset_dialog,
-          &EditTandemPresetDialog::accepted,
-          this,
+  connect(_p_preset_dialog, &EditTandemPresetDialog::accepted, this,
           &TandemRunDialog::acceptPresetEdit);
-  connect(_p_preset_dialog,
-          &EditTandemPresetDialog::rejected,
-          this,
+  connect(_p_preset_dialog, &EditTandemPresetDialog::rejected, this,
           &TandemRunDialog::rejectPresetEdit);
 #else
   // Qt4 code
@@ -316,9 +312,7 @@ TandemRunDialog::selectFastaFiles()
         settings.value("path/tandemrun_fastafiles_directory", "").toString();
 
       QStringList filenames = QFileDialog::getOpenFileNames(
-        this,
-        tr("FASTA files"),
-        default_fasta_location,
+        this, tr("FASTA files"), default_fasta_location,
         tr("FASTA files (*.fasta);;all files (*)"));
 
       if(filenames.size() > 0)
@@ -349,8 +343,7 @@ TandemRunDialog::selectXtandemExe()
 
 
       QString filename =
-        QFileDialog::getOpenFileName(this,
-                                     tr("select X!Tandem executable"),
+        QFileDialog::getOpenFileName(this, tr("select X!Tandem executable"),
                                      QDir(tandem_bin_path).absolutePath(),
                                      tr("all files (*);;exe files (*.exe)"));
       fillTandemBinPath(filename, true);
@@ -373,9 +366,7 @@ TandemRunDialog::selectMzFiles()
         settings.value("path/tandemrun_mzfiles_directory", "").toString();
 
       QStringList filenames = QFileDialog::getOpenFileNames(
-        this,
-        tr("select peak list files"),
-        default_mz_location,
+        this, tr("select peak list files"), default_mz_location,
         tr("any mz files (*.mzXML *.mzxml *.mzML *.mzml *.mgf);;mzXML (*.mzXML "
            "*.mzxml);;mzML (*.mzML *.mzml);;MGF (*.mgf);;all files (*)"));
 
@@ -518,8 +509,7 @@ TandemRunDialog::fillTandemBinPath(const QString &tandem_bin_path_in,
       else
         {
           QMessageBox::warning(
-            this,
-            tr("Wrong X!Tandem exe file"),
+            this, tr("Wrong X!Tandem exe file"),
             tr("%1 is not executable.").arg(tandem_bin_path));
         }
     }
@@ -540,8 +530,7 @@ TandemRunDialog::checkXtandemBin()
   if(tandem_bin_path.isEmpty())
     {
       QMessageBox::warning(
-        this,
-        tr("Wrong X!Tandem configuration"),
+        this, tr("Wrong X!Tandem configuration"),
         tr("X!Tandem .exe file is not set.\n%1").arg(tandem_install_text));
 
       QDesktopServices::openUrl(QUrl("https://www.thegpm.org/tandem/"));
@@ -561,8 +550,7 @@ TandemRunDialog::checkXtandemBin()
           catch(pappso::PappsoException &error)
             {
               QMessageBox::warning(
-                this,
-                tr("Wrong X!Tandem exe file"),
+                this, tr("Wrong X!Tandem exe file"),
                 tr("%1 does not seem to be a valid X!Tandem version.\n%2")
                   .arg(tandem_bin.absoluteFilePath())
                   .arg(tandem_install_text));
@@ -572,8 +560,7 @@ TandemRunDialog::checkXtandemBin()
         }
       else
         {
-          QMessageBox::warning(this,
-                               tr("Wrong X!Tandem exe file"),
+          QMessageBox::warning(this, tr("Wrong X!Tandem exe file"),
                                tr("%1 is not executable.\n%2")
                                  .arg(tandem_bin_path)
                                  .arg(tandem_install_text));
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.h b/src/gui/tandem_run_dialog/tandemrundialog.h
index 45e234b8dc8973b9a268087ff78dc940289be3db..5bc76507a3e1c3f62ec34340a8f0f765fc8675df 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.h
+++ b/src/gui/tandem_run_dialog/tandemrundialog.h
@@ -33,7 +33,7 @@
 
 namespace Ui
 {
-class TandemRunDialog;
+  class TandemRunDialog;
 }
 
 
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.h b/src/gui/waiting_message_dialog/waitingmessagedialog.h
index a20c256b4f948fbe4630a7eaef5857aad3c85493..50a73da76796de26bf466165342ef5658bdad11c 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.h
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.h
@@ -34,7 +34,7 @@
 
 namespace Ui
 {
-class WaitingMessageDialog;
+  class WaitingMessageDialog;
 }
 
 
diff --git a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
index 5b2fa39f16c63b72da273a2264ac2422838c54ea..a01b80525f1ec1fe1c66eb6068af61c41b67c56e 100644
--- a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
+++ b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
@@ -31,7 +31,7 @@
 
 namespace Ui
 {
-class AutomaticFilterWidget;
+  class AutomaticFilterWidget;
 }
 
 class AutomaticFilterWidget : public QWidget
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
index 5e167b1d412d6634df54a93d5826ec17823ba556..530668ffa3fcf7bf914c128fc5d461a6633aeff7 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
@@ -215,9 +215,7 @@ ContaminantWidget::doSelectFastaFile()
         settings.value("path/fastafiles_directory", "").toString();
 
       QStringList filenames = QFileDialog::getOpenFileNames(
-        this,
-        tr("FASTA files"),
-        default_fasta_location,
+        this, tr("FASTA files"), default_fasta_location,
         tr("FASTA files (*.fasta);;all files (*)"));
 
       if(filenames.size() > 0)
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.h b/src/gui/widgets/contaminant_widget/contaminantwidget.h
index 0a79d0958293439de1ff3cf7068ad29bd5646394..ffea09bd5da7ae97c8c5da086fb3b29eea72cae3 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.h
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.h
@@ -40,7 +40,7 @@
 
 namespace Ui
 {
-class ContaminantWidget;
+  class ContaminantWidget;
 }
 
 class ContaminantWidget : public QWidget
diff --git a/src/gui/widgets/decoy_widget/decoywidget.cpp b/src/gui/widgets/decoy_widget/decoywidget.cpp
index b2289982aa8d74e6c1012354d66238d43859f2bf..d627f397a4b85acb55af18cba69bca15885d2947 100644
--- a/src/gui/widgets/decoy_widget/decoywidget.cpp
+++ b/src/gui/widgets/decoy_widget/decoywidget.cpp
@@ -224,9 +224,7 @@ DecoyWidget::doSelectFastaFile()
         settings.value("path/fastafiles_directory", "").toString();
 
       QStringList filenames = QFileDialog::getOpenFileNames(
-        this,
-        tr("FASTA files"),
-        default_fasta_location,
+        this, tr("FASTA files"), default_fasta_location,
         tr("FASTA files (*.fasta);;all files (*)"));
 
       if(filenames.size() > 0)
diff --git a/src/gui/widgets/decoy_widget/decoywidget.h b/src/gui/widgets/decoy_widget/decoywidget.h
index 9cd64c78643b8f0b568b7c24498611b137df46af..4406058d17bc7acbbb4188a27d8b2945a9990422 100644
--- a/src/gui/widgets/decoy_widget/decoywidget.h
+++ b/src/gui/widgets/decoy_widget/decoywidget.h
@@ -36,7 +36,7 @@
 
 namespace Ui
 {
-class DecoyWidget;
+  class DecoyWidget;
 }
 
 class DecoyWidget : public QWidget
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index f432d576d8ebf3284dc97846fcbca0ab6d60f701..118a7f4bc56c48635ab2a8b12153428233230f15 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -58,182 +58,106 @@ WorkerThread::WorkerThread(MainWindow *p_main_window)
 #if QT_VERSION >= 0x050000
   // Qt5 code
   // worker message
-  connect(_p_work_monitor,
-          &WorkMonitor::workerMessage,
-          p_main_window,
+  connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,
           &MainWindow::doDisplayLoadingMessage);
-  connect(_p_work_monitor,
-          &WorkMonitor::workerMessagePercent,
-          p_main_window,
+  connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,
           &MainWindow::doDisplayLoadingMessagePercent);
-  connect(_p_work_monitor,
-          &WorkMonitor::workerAppendText,
-          p_main_window,
+  connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,
           &MainWindow::doWorkerAppendText);
-  connect(_p_work_monitor,
-          &WorkMonitor::workerSetText,
-          p_main_window,
+  connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,
           &MainWindow::doWorkerSetText);
-  connect(_p_work_monitor,
-          &WorkMonitor::workerJobFinished,
-          p_main_window,
+  connect(_p_work_monitor, &WorkMonitor::workerJobFinished, p_main_window,
           &MainWindow::doDisplayJobFinished);
 
-  connect(p_main_window,
-          &MainWindow::operateXpipFile,
-          this,
+  connect(p_main_window, &MainWindow::operateXpipFile, this,
           &WorkerThread::doXpipFileLoad);
-  connect(p_main_window,
-          &MainWindow::operateWritingXpipFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingXpipFile, this,
           &WorkerThread::doWritingXpipFile);
-  connect(this,
-          &WorkerThread::projectReady,
-          p_main_window,
+  connect(this, &WorkerThread::projectReady, p_main_window,
           &MainWindow::doProjectReady);
-  connect(this,
-          &WorkerThread::loadingResultsFinished,
-          p_main_window,
+  connect(this, &WorkerThread::loadingResultsFinished, p_main_window,
           &MainWindow::doLoadingResultsReady);
 
-  connect(p_main_window,
-          &MainWindow::operateLoadingResults,
-          this,
+  connect(p_main_window, &MainWindow::operateLoadingResults, this,
           &WorkerThread::doLoadingResults);
 
-  connect(p_main_window,
-          &MainWindow::operateRunningXtandem,
-          this,
+  connect(p_main_window, &MainWindow::operateRunningXtandem, this,
           &WorkerThread::doRunningXtandem);
-  connect(this,
-          &WorkerThread::loadingMessage,
-          p_main_window,
+  connect(this, &WorkerThread::loadingMessage, p_main_window,
           &MainWindow::doDisplayLoadingMessage);
-  connect(this,
-          &WorkerThread::projectNotReady,
-          p_main_window,
+  connect(this, &WorkerThread::projectNotReady, p_main_window,
           &MainWindow::doProjectNotReady);
 
   // grouping
-  connect(p_main_window,
-          &MainWindow::operateGrouping,
-          this,
+  connect(p_main_window, &MainWindow::operateGrouping, this,
           &WorkerThread::doGrouping);
-  connect(this,
-          &WorkerThread::groupingFinished,
-          p_main_window,
+  connect(this, &WorkerThread::groupingFinished, p_main_window,
           &MainWindow::doGroupingFinished);
   // masschroq write
-  connect(p_main_window,
-          &MainWindow::operateWritingMassChroqFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,
           &WorkerThread::doWritingMassChroqFile);
-  connect(p_main_window,
-          &MainWindow::operateWritingMassChroqPrmFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,
           &WorkerThread::doWritingMassChroqPrmFile);
-  connect(p_main_window,
-          &MainWindow::operateWritingMcqrSpectralCountFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingMcqrSpectralCountFile, this,
           &WorkerThread::doWritingMcqrSpectralCountFile);
   // protic write
-  connect(p_main_window,
-          &MainWindow::operateWritingProticFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingProticFile, this,
           &WorkerThread::doWritingProticFile);
   // writing ODS file :
-  connect(p_main_window,
-          &MainWindow::operateWritingOdsFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingOdsFile, this,
           &WorkerThread::doWritingOdsFile);
-  connect(this,
-          &WorkerThread::operationFailed,
-          p_main_window,
+  connect(this, &WorkerThread::operationFailed, p_main_window,
           &MainWindow::doOperationFailed);
-  connect(this,
-          &WorkerThread::operationFinished,
-          p_main_window,
+  connect(this, &WorkerThread::operationFinished, p_main_window,
           &MainWindow::doOperationFinished);
   // FASTA file write
-  connect(p_main_window,
-          &MainWindow::operateWritingFastaFile,
-          this,
+  connect(p_main_window, &MainWindow::operateWritingFastaFile, this,
           &WorkerThread::doWritingFastaFile);
 
 #else
   // Qt4 code
   // worker message
-  connect(_p_work_monitor,
-          SIGNAL(workerMessage(QString)),
-          p_main_window,
+  connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,
           SLOT(doDisplayLoadingMessage(QString)));
-  connect(_p_work_monitor,
-          SIGNAL(workerMessage(QString, int)),
-          p_main_window,
+  connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,
           SLOT(doDisplayLoadingMessage(QString, int)));
-  connect(_p_work_monitor,
-          SIGNAL(workerAppendText(char *)),
-          p_main_window,
+  connect(_p_work_monitor, SIGNAL(workerAppendText(char *)), p_main_window,
           SLOT(doWorkerAppendText(char *)));
 
-  connect(p_main_window,
-          SIGNAL(operateXpipFile(QString)),
-          this,
+  connect(p_main_window, SIGNAL(operateXpipFile(QString)), this,
           SLOT(doXpipFileLoad(QString)));
-  connect(this,
-          SIGNAL(projectReady(ProjectSp)),
-          p_main_window,
+  connect(this, SIGNAL(projectReady(ProjectSp)), p_main_window,
           SLOT(doProjectReady(ProjectSp)));
   connect(
     p_main_window,
     SIGNAL(operateLoadingResults(bool, AutomaticFilterParameters, QStringList)),
-    this,
-    SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
+    this, SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
 
-  connect(p_main_window,
-          SIGNAL(operateRunningXtandem(TandemRunBatch)),
-          this,
+  connect(p_main_window, SIGNAL(operateRunningXtandem(TandemRunBatch)), this,
           SLOT(doRunningXtandem(TandemRunBatch)));
-  connect(this,
-          SIGNAL(loadingMessage(QString)),
-          p_main_window,
+  connect(this, SIGNAL(loadingMessage(QString)), p_main_window,
           SLOT(doDisplayLoadingMessage(QString)));
-  connect(this,
-          SIGNAL(projectNotReady(QString)),
-          p_main_window,
+  connect(this, SIGNAL(projectNotReady(QString)), p_main_window,
           SLOT(doProjectNotReady(QString)));
 
   // grouping
-  connect(p_main_window,
-          SIGNAL(operateGrouping(ProjectSp)),
-          this,
+  connect(p_main_window, SIGNAL(operateGrouping(ProjectSp)), this,
           SLOT(doGrouping(ProjectSp)));
-  connect(this,
-          SIGNAL(groupingFinished()),
-          p_main_window,
+  connect(this, SIGNAL(groupingFinished()), p_main_window,
           SLOT(doGroupingFinished()));
   // masschroq write
   connect(p_main_window,
-          SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)),
-          this,
+          SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,
           SLOT(doWritingMassChroqFile(QString, ProjectSp)));
   // protic write
-  connect(p_main_window,
-          SIGNAL(operateWritingProticFile(QString, ProjectSp)),
-          this,
-          SLOT(doWritingProticFile(QString, ProjectSp)));
+  connect(p_main_window, SIGNAL(operateWritingProticFile(QString, ProjectSp)),
+          this, SLOT(doWritingProticFile(QString, ProjectSp)));
   // writing ODS file :
-  connect(p_main_window,
-          SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
-          this,
-          SLOT(doWritingOdsFile(QString, ProjectSp)));
-  connect(this,
-          SIGNAL(operationFailed(QString)),
-          p_main_window,
+  connect(p_main_window, SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
+          this, SLOT(doWritingOdsFile(QString, ProjectSp)));
+  connect(this, SIGNAL(operationFailed(QString)), p_main_window,
           SLOT(doOperationFailed(QString)));
-  connect(this,
-          SIGNAL(operationFinished()),
-          p_main_window,
+  connect(this, SIGNAL(operationFinished()), p_main_window,
           SLOT(doOperationFinished()));
 #endif
 
@@ -250,56 +174,34 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
   // Qt5 code
 
   // worker message
-  connect(_p_work_monitor,
-          &WorkMonitor::workerMessage,
-          p_project_window,
+  connect(_p_work_monitor, &WorkMonitor::workerMessage, p_project_window,
           &ProjectWindow::doDisplayLoadingMessage);
-  connect(_p_work_monitor,
-          &WorkMonitor::workerMessagePercent,
-          p_project_window,
+  connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_project_window,
           &ProjectWindow::doDisplayLoadingMessagePercent);
-  connect(this,
-          &WorkerThread::loadingMessage,
-          p_project_window,
+  connect(this, &WorkerThread::loadingMessage, p_project_window,
           &ProjectWindow::doDisplayLoadingMessage);
   // grouping
-  connect(p_project_window,
-          &ProjectWindow::operateGrouping,
-          this,
+  connect(p_project_window, &ProjectWindow::operateGrouping, this,
           &WorkerThread::doGrouping);
-  connect(this,
-          &WorkerThread::groupingFinished,
-          p_project_window,
+  connect(this, &WorkerThread::groupingFinished, p_project_window,
           &ProjectWindow::doGroupingFinished);
 
 
   // PTM grouping on IdentificationGroup
-  connect(p_project_window,
-          &ProjectWindow::operatePtmGroupingOnIdentification,
-          this,
-          &WorkerThread::doPtmGroupingOnIdentification);
-  connect(this,
-          &WorkerThread::ptmGroupingOnIdentificationFinished,
-          p_project_window,
-          &ProjectWindow::refreshPtmGroup);
+  connect(p_project_window, &ProjectWindow::operatePtmGroupingOnIdentification,
+          this, &WorkerThread::doPtmGroupingOnIdentification);
+  connect(this, &WorkerThread::ptmGroupingOnIdentificationFinished,
+          p_project_window, &ProjectWindow::refreshPtmGroup);
 
   // grouping on IdentificationGroup
-  connect(p_project_window,
-          &ProjectWindow::operateGroupingOnIdentification,
-          this,
-          &WorkerThread::doGroupingOnIdentification);
-  connect(this,
-          &WorkerThread::groupingOnIdentificationFinished,
-          p_project_window,
-          &ProjectWindow::refreshGroup);
+  connect(p_project_window, &ProjectWindow::operateGroupingOnIdentification,
+          this, &WorkerThread::doGroupingOnIdentification);
+  connect(this, &WorkerThread::groupingOnIdentificationFinished,
+          p_project_window, &ProjectWindow::refreshGroup);
 
-  connect(this,
-          &WorkerThread::operationFailed,
-          p_project_window,
+  connect(this, &WorkerThread::operationFailed, p_project_window,
           &ProjectWindow::doOperationFailed);
-  connect(this,
-          &WorkerThread::operationFinished,
-          p_project_window,
+  connect(this, &WorkerThread::operationFinished, p_project_window,
           &ProjectWindow::doOperationFinished);
 
 #else
@@ -307,39 +209,27 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
   // worker message
-  connect(_p_work_monitor,
-          SIGNAL(workerMessage(QString)),
-          p_project_window,
+  connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,
           SLOT(doDisplayLoadingMessage(QString)));
-  connect(_p_work_monitor,
-          SIGNAL(workerMessage(QString, int)),
-          p_project_window,
-          SLOT(doDisplayLoadingMessage(QString, int)));
+  connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)),
+          p_project_window, SLOT(doDisplayLoadingMessage(QString, int)));
 
-  connect(this,
-          SIGNAL(loadingMessage(QString)),
-          p_project_window,
+  connect(this, SIGNAL(loadingMessage(QString)), p_project_window,
           SLOT(doDisplayLoadingMessage(QString)));
   // grouping
-  connect(p_project_window,
-          SIGNAL(operateGrouping(ProjectSp)),
-          this,
+  connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,
           SLOT(doGrouping(ProjectSp)));
-  connect(this,
-          SIGNAL(groupingFinished()),
-          p_project_window,
+  connect(this, SIGNAL(groupingFinished()), p_project_window,
           SLOT(doGroupingFinished()));
 
 
   // PTM grouping on IdentificationGroup
   connect(p_project_window,
           SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)),
-          this,
-          SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
+          this, SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
   connect(this,
           SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)),
-          p_project_window,
-          SLOT(refreshPtmGroup(IdentificationGroup *)));
+          p_project_window, SLOT(refreshPtmGroup(IdentificationGroup *)));
 
   // grouping on IdentificationGroup
   connect(
@@ -348,18 +238,12 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
       operateGroupingOnIdentification(IdentificationGroup *, GroupingType)),
     this,
     SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
-  connect(this,
-          SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
-          p_project_window,
-          SLOT(refreshGroup(IdentificationGroup *)));
+  connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
+          p_project_window, SLOT(refreshGroup(IdentificationGroup *)));
 
-  connect(this,
-          SIGNAL(operationFailed(QString)),
-          p_project_window,
+  connect(this, SIGNAL(operationFailed(QString)), p_project_window,
           SLOT(doOperationFailed(QString)));
-  connect(this,
-          SIGNAL(operationFinished()),
-          p_project_window,
+  connect(this, SIGNAL(operationFinished()), p_project_window,
           SLOT(doOperationFinished()));
 
 #endif
@@ -511,8 +395,7 @@ WorkerThread::doWritingXpipFile(QString filename, ProjectSp project_sp)
     }
 }
 void
-WorkerThread::doWritingOdsFile(QString filename,
-                               QString format,
+WorkerThread::doWritingOdsFile(QString filename, QString format,
                                ProjectSp project_sp)
 {
 
@@ -547,8 +430,7 @@ WorkerThread::doWritingOdsFile(QString filename,
 
 
 void
-WorkerThread::doWritingMassChroqFile(QString filename,
-                                     ProjectSp project_sp,
+WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp,
                                      MasschroqFileParameters params)
 {
 
@@ -716,14 +598,14 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
 
       if(use_htcondor)
         {
-          TandemCondorProcess xt_process(
-            _p_main_window, _p_work_monitor, tandem_run_batch);
+          TandemCondorProcess xt_process(_p_main_window, _p_work_monitor,
+                                         tandem_run_batch);
           xt_process.run();
         }
       else
         {
-          TandemBatchProcess xt_process(
-            _p_main_window, _p_work_monitor, tandem_run_batch);
+          TandemBatchProcess xt_process(_p_main_window, _p_work_monitor,
+                                        tandem_run_batch);
           xt_process.run();
         }
 
@@ -741,8 +623,7 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
 
 
 void
-WorkerThread::doWritingFastaFile(QString filename,
-                                 ProjectSp project_sp,
+WorkerThread::doWritingFastaFile(QString filename, ProjectSp project_sp,
                                  ExportFastaType type)
 {
 
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 42c9ced2e82c03f37227e61f0de5b7aaf60893d5..3929b9d2f0015a4842d1d810e14895211d6c1255 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -57,19 +57,16 @@ class WorkerThread : public QObject
 
   public slots:
   void doXpipFileLoad(QString filename);
-  void doLoadingResults(bool is_individual,
-                        AutomaticFilterParameters param,
+  void doLoadingResults(bool is_individual, AutomaticFilterParameters param,
                         QStringList file_list);
   void doWritingXpipFile(QString filename, ProjectSp project_sp);
   void doWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
-  void doWritingMassChroqFile(QString filename,
-                              ProjectSp project_sp,
+  void doWritingMassChroqFile(QString filename, ProjectSp project_sp,
                               MasschroqFileParameters params);
   void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
   void doWritingProticFile(QString filename, ProjectSp project_sp);
   void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
-  void doWritingFastaFile(QString filename,
-                          ProjectSp project_sp,
+  void doWritingFastaFile(QString filename, ProjectSp project_sp,
                           ExportFastaType type);
   void doGrouping(ProjectSp project_sp);
   void doGroupingOnIdentification(IdentificationGroup *p_identification_group,
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 070f061dbd5f3f2970114a540e88a8b35cde0d84..efd25ee93eb1659e0e898b0c66b6364e28693592 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -139,17 +139,13 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
   connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
 
 
-  connect(this,
-          &XicBox::computeIsotopeMassList,
-          p_worker,
+  connect(this, &XicBox::computeIsotopeMassList, p_worker,
           &XicWorkerThread::doComputeIsotopeMassList);
-  connect(p_worker,
-          &XicWorkerThread::isotopeMassListComputed,
-          this,
+  connect(p_worker, &XicWorkerThread::isotopeMassListComputed, this,
           &XicBox::setIsotopeMassList);
 
-  connect(
-    _p_xic_window, &XicWindow::reExtractXicNeeded, this, &XicBox::reExtractXic);
+  connect(_p_xic_window, &XicWindow::reExtractXicNeeded, this,
+          &XicBox::reExtractXic);
   /*  connect(ui->xic_widget,
           qOverload<std::vector<std::pair<pappso::XicCstSPtr,
   pappso::XicPeakSp>>>( &pappso::XicWidget::xicPeakListChanged), this,
@@ -160,9 +156,7 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
           this,
           &XicBox::onXicWidgetClick);
 */
-  connect(_p_xic_window,
-          &XicWindow::rtUnitChangeNeeded,
-          this,
+  connect(_p_xic_window, &XicWindow::rtUnitChangeNeeded, this,
           &XicBox::onRtUnitChanged);
 #else
 // Qt4 code
@@ -270,15 +264,13 @@ XicBox::setPeptideEvidence(const PeptideEvidence *p_peptide_evidence)
   _p_xic_window->getProjectWindow()
     ->getProjectP()
     ->getSameXicPeptideEvidenceList(
-      _peptide_evidence_list,
-      _msrun_sp.get(),
+      _peptide_evidence_list, _msrun_sp.get(),
       _p_peptide_evidence->getPeptideXtpSp().get(),
       _p_peptide_evidence->getCharge());
 
   emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
                               _p_peptide_evidence->getCharge(),
-                              _p_xic_window->getXicExtractPrecision(),
-                              0.8);
+                              _p_xic_window->getXicExtractPrecision(), 0.8);
 }
 
 void
@@ -303,8 +295,7 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
   _p_xic_window->getProjectWindow()
     ->getProjectP()
     ->getSameXicPeptideEvidenceList(
-      _peptide_evidence_list,
-      _msrun_sp.get(),
+      _peptide_evidence_list, _msrun_sp.get(),
       _p_peptide_evidence->getPeptideXtpSp().get(),
       _p_peptide_evidence->getCharge());
   //_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence,
@@ -312,8 +303,7 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
 
   emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
                               _p_peptide_evidence->getCharge(),
-                              _p_xic_window->getXicExtractPrecision(),
-                              0.8);
+                              _p_xic_window->getXicExtractPrecision(), 0.8);
 }
 
 void
@@ -506,9 +496,7 @@ XicBox::setIsotopeMassList(
         {nullptr, natural_isotope_average, nullptr, nullptr});
     }
 
-  emit loadXic(_msrun_sp,
-               mass_list,
-               _p_xic_window->getXicExtractPrecision(),
+  emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
                pappso::XicExtractMethod::max);
 
   // histogram
@@ -582,9 +570,7 @@ XicBox::reExtractXic()
       mass_list.push_back(
         xic_isotope.peptide_natural_isotope_sp.get()->getMz());
     }
-  emit loadXic(_msrun_sp,
-               mass_list,
-               _p_xic_window->getXicExtractPrecision(),
+  emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
                pappso::XicExtractMethod::max);
   qDebug() << "XicBox::reExtractXic end";
 }
@@ -597,7 +583,8 @@ XicBox::setRetentionTime(double rt)
 }
 void
 XicBox::setXicPeakList(
-  std::vector<std::pair<pappso::XicCstSPtr, pappso::XicPeakCstSPtr>> xic_peak_list)
+  std::vector<std::pair<pappso::XicCstSPtr, pappso::XicPeakCstSPtr>>
+    xic_peak_list)
 {
   qDebug() << "XicBox::setXicPeakList begin";
   QString html;
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index b7acc1f17ddb35c369728bcff7df72265d495bdc..7c8fb86e2b664ef4d01819d0903880530db592ef 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -40,7 +40,7 @@
 
 namespace Ui
 {
-class XicBox;
+  class XicBox;
 }
 
 
@@ -67,12 +67,9 @@ class XicBox : public QWidget
                                  MsRunSp msrun_sp);
 
   signals:
-  void loadXic(MsRunSp p_msrun,
-               std::vector<pappso::pappso_double> mz_list,
-               pappso::PrecisionPtr precision,
-               pappso::XicExtractMethod method);
-  void computeIsotopeMassList(pappso::PeptideSp peptide_sp,
-                              unsigned int charge,
+  void loadXic(MsRunSp p_msrun, std::vector<pappso::pappso_double> mz_list,
+               pappso::PrecisionPtr precision, pappso::XicExtractMethod method);
+  void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge,
                               pappso::PrecisionPtr precision,
                               double minimum_isotope_pattern_ratio);
   private slots:
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index bc48fe3fc7336a65ede8be7fdb1e3076d2ea920b..86d507b5c192c936b0565802351e4e33a42bfc71 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/src/gui/xic_view/xic_widgets/zivywidget.h
@@ -34,7 +34,7 @@
 
 namespace Ui
 {
-class ZivyWidget;
+  class ZivyWidget;
 }
 
 
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index e4ea183905fe3289721c139b6271f5e1a4f38a1f..51cf71c93d8eac0263b6f46f10410aee5c677d24 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -57,9 +57,7 @@ XicWindow::XicWindow(ProjectWindow *parent)
   _p_zivy_dialog->setZivyParams(zivy_params);
 
 
-  connect(_p_zivy_dialog,
-          &ZivyDialog::accepted,
-          this,
+  connect(_p_zivy_dialog, &ZivyDialog::accepted, this,
           &XicWindow::doAcceptedZivyDialog);
 
 #if QT_VERSION >= 0x050000
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index a83ae03b3228be55fdb7fffe724c53effd6e2636..22d49a1c2ca3cedb4b2e1d27c651d5326cb5500f 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -43,7 +43,7 @@ class ProjectWindow;
 
 namespace Ui
 {
-class XicWindow;
+  class XicWindow;
 }
 
 class XicBox;
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 6aef044af1398066aa06efc8d76707c7d5935aeb..6c636f40c0a67773f4a53b5f8fe1cd47d91097b5 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -98,8 +98,7 @@ XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
       isotope_mass_list = isotope_list.getByIntensityRatio(
         charge, precision, minimum_isotope_pattern_ratio);
 
-      std::sort(isotope_mass_list.begin(),
-                isotope_mass_list.end(),
+      std::sort(isotope_mass_list.begin(), isotope_mass_list.end(),
                 [](const pappso::PeptideNaturalIsotopeAverageSp &m,
                    const pappso::PeptideNaturalIsotopeAverageSp &n) -> bool {
                   unsigned int mn(m.get()->getIsotopeNumber()),
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index bb9cffb8ef63aee3c929713539295818358c7527..2bb662fb04f0e74b653694dc1ae41f5875a0b093 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -43,8 +43,7 @@ class XicWorkerThread : public QObject
   XicWorkerThread(XicBox *parent);
   virtual ~XicWorkerThread();
   public slots:
-  void doXicLoad(MsRunSp p_msrun,
-                 std::vector<pappso::pappso_double> mz_list,
+  void doXicLoad(MsRunSp p_msrun, std::vector<pappso::pappso_double> mz_list,
                  pappso::PrecisionPtr precision,
                  pappso::XicExtractMethod method);
   void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
diff --git a/src/input/condorqxmlsaxhandler.cpp b/src/input/condorqxmlsaxhandler.cpp
index 726e9b8b6f14625cc9aa756261bc6763cfb2eb6b..0b7081d3794435b5d0297cdc249768636bedc0be 100644
--- a/src/input/condorqxmlsaxhandler.cpp
+++ b/src/input/condorqxmlsaxhandler.cpp
@@ -72,18 +72,16 @@ CondorQxmlSaxHandler::startElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in CondorQxmlSaxHandler::startElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in CondorQxmlSaxHandler::startElement tag "
-                    "%1, std exception:\n%2")
+      _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
+                              "%1, std exception:\n%2")
                     .arg(qName)
                     .arg(exception_std.what());
       return false;
@@ -93,8 +91,7 @@ CondorQxmlSaxHandler::startElement(const QString &namespaceURI,
 
 bool
 CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
-                                 const QString &localName,
-                                 const QString &qName)
+                                 const QString &localName, const QString &qName)
 {
 
   bool is_ok = true;
@@ -121,18 +118,16 @@ CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in CondorQxmlSaxHandler::endElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in CondorQxmlSaxHandler::endElement tag "
-                    "%1, std exception:\n%2")
+      _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
+                              "%1, std exception:\n%2")
                     .arg(qName)
                     .arg(exception_std.what());
       return false;
@@ -148,9 +143,8 @@ CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
 bool
 CondorQxmlSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -162,9 +156,8 @@ CondorQxmlSaxHandler::error(const QXmlParseException &exception)
 bool
 CondorQxmlSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/condorqxmlsaxhandler.h b/src/input/condorqxmlsaxhandler.h
index 9b2e05b9f18e60373a3e25cb0175874c06b02778..4fd269c619fbc50a0cead5d997c9ec4688816fe6 100644
--- a/src/input/condorqxmlsaxhandler.h
+++ b/src/input/condorqxmlsaxhandler.h
@@ -55,13 +55,10 @@ class CondorQxmlSaxHandler : public QXmlDefaultHandler
   CondorQxmlSaxHandler(TandemCondorProcess *tandem_condor_process);
   ~CondorQxmlSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 73b854753f830fa82c465ba0b2eca6d5dd475f66..9cc1dafc62a95eb59c73597dedcf2e8368332edf 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -252,8 +252,7 @@ getQVariantDoubleParam(pwiz::data::ParamContainer *item, pwiz::cv::CVID param)
 
 void
 IdentificationPwizReader::read(
-  IdentificationDataSource *p_identification_data_source,
-  Project *p_project,
+  IdentificationDataSource *p_identification_data_source, Project *p_project,
   IdentificationGroup *p_identification_group)
 {
   qDebug() << "IdentificationPwizReader::read begin";
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index 7ed1fde50bd9ee5fbc7d821bddc35652d02a8e37..4738d65f668345c032277e8bbcc3090786ad65f6 100644
--- a/src/input/identificationpwizreader.h
+++ b/src/input/identificationpwizreader.h
@@ -42,10 +42,10 @@
 
 namespace pwiz
 {
-namespace identdata
-{
-  class IdentDataFile;
-}
+  namespace identdata
+  {
+    class IdentDataFile;
+  }
 } // namespace pwiz
 
 class IdentificationPwizReader
@@ -57,8 +57,7 @@ class IdentificationPwizReader
   IdentificationEngine getIdentificationEngine() const;
 
   void read(IdentificationDataSource *p_identification_data_source,
-            Project *p_project,
-            IdentificationGroup *p_identification_group);
+            Project *p_project, IdentificationGroup *p_identification_group);
 
   private:
   IdentificationEngine getIdentificationEngine(const QString &xml_id) const;
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index eb4e5c8dc00e53a594ef4dcf2ce05d72c6586865..e0ea73b2a1f98beefdfcc4b9ea29ccc3c4737b9d 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -38,8 +38,7 @@
 #include "../../core/peptideevidence.h"
 
 MascotDatParser::MascotDatParser(
-  Project *p_project,
-  IdentificationGroup *p_identification_group,
+  Project *p_project, IdentificationGroup *p_identification_group,
   IdentificationDataSource *p_identification_data_source)
 {
   _p_project                    = p_project;
@@ -551,9 +550,8 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
 
   catch(pappso::PappsoException exception_pappso)
     {
-      _error_str = QObject::tr(
-                     "ERROR in MascotDatParser::parsePeptidesLine "
-                     "%1, PAPPSO exception:\n%2 near q%3_p%4")
+      _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
+                               "%1, PAPPSO exception:\n%2 near q%3_p%4")
                      .arg(peptide_line)
                      .arg(exception_pappso.qwhat())
                      .arg(_current_peptide.query_index)
@@ -563,13 +561,13 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
     }
   catch(std::exception exception_std)
     {
-      _error_str = QObject::tr(
-                     "ERROR in MascotDatParser::parsePeptidesLine %1, std "
-                     "exception:\n%2  near q%3_p%4")
-                     .arg(peptide_line)
-                     .arg(exception_std.what())
-                     .arg(_current_peptide.query_index)
-                     .arg(_current_peptide.peptide_index);
+      _error_str =
+        QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, std "
+                    "exception:\n%2  near q%3_p%4")
+          .arg(peptide_line)
+          .arg(exception_std.what())
+          .arg(_current_peptide.query_index)
+          .arg(_current_peptide.peptide_index);
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
     }
@@ -639,11 +637,11 @@ MascotDatParser::parseQueryLine(const QString &query_line)
 
   catch(pappso::PappsoException exception_pappso)
     {
-      _error_str = QObject::tr(
-                     "ERROR in MascotDatParser::parseQueryLine %1, PAPPSO "
-                     "exception:\n%2")
-                     .arg(query_line)
-                     .arg(exception_pappso.qwhat());
+      _error_str =
+        QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, PAPPSO "
+                    "exception:\n%2")
+          .arg(query_line)
+          .arg(exception_pappso.qwhat());
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
     }
@@ -848,15 +846,13 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
             {
               peptide_evidence.setEvalue(getEvalue(
                 ion_score,
-                _decoy_summary_list.at(_current_query.query_index - 1),
-                0.05));
+                _decoy_summary_list.at(_current_query.query_index - 1), 0.05));
             }
           else
             {
-              peptide_evidence.setEvalue(
-                getEvalue(ion_score,
-                          _summary_list.at(_current_query.query_index - 1),
-                          0.05));
+              peptide_evidence.setEvalue(getEvalue(
+                ion_score, _summary_list.at(_current_query.query_index - 1),
+                0.05));
             }
 
           peptide_evidence.setParam(
@@ -988,18 +984,16 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
 
   catch(pappso::PappsoException exception_pappso)
     {
-      _error_str = QObject::tr(
-                     "ERROR in MascotDatParser::savePeptideList "
-                     " PAPPSO exception:\n%2")
+      _error_str = QObject::tr("ERROR in MascotDatParser::savePeptideList "
+                               " PAPPSO exception:\n%2")
                      .arg(exception_pappso.qwhat());
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
     }
   catch(std::exception exception_std)
     {
-      _error_str = QObject::tr(
-                     "ERROR in MascotDatParser::savePeptideList std "
-                     "exception:\n%2")
+      _error_str = QObject::tr("ERROR in MascotDatParser::savePeptideList std "
+                               "exception:\n%2")
                      .arg(exception_std.what());
       qDebug() << _error_str;
       throw pappso::PappsoException(_error_str);
@@ -1025,8 +1019,7 @@ MascotDatParser::getEvalue(pappso::pappso_double ion_score,
 
 pappso::pappso_double
 MascotDatParser::getEvalueExperimental(
-  pappso::pappso_double ion_score,
-  SummaryLine &summary_line,
+  pappso::pappso_double ion_score, SummaryLine &summary_line,
   pappso::pappso_double confidence_interval) const
 {
   // Evalue experimental  Homology threshold (QPlughole value from .dat file).
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index d34368738e1a5130f6a14205393e8c6a760f7742..3268d523aaa1c17ec2469c173d1bda25d2522515 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -89,8 +89,7 @@ class MascotDatParser
   };
   void savePeptideList(std::vector<PeptideLine> &peptide_list, bool is_decoy);
   pappso::pappso_double
-  getEvalue(pappso::pappso_double ion_score,
-            SummaryLine &summary_line,
+  getEvalue(pappso::pappso_double ion_score, SummaryLine &summary_line,
             pappso::pappso_double confidence_interval = 0.05) const;
   pappso::pappso_double
   getEvalueExperimental(pappso::pappso_double ion_score,
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index bc0ad83d350152e342dda7c1249d7caf2240a82a..af6b1be03d7b127fa576f612a1bbe361d597d011 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -38,8 +38,7 @@
 
 
 PepXmlSaxHandler::PepXmlSaxHandler(
-  Project *p_project,
-  IdentificationGroup *p_identification_group,
+  Project *p_project, IdentificationGroup *p_identification_group,
   IdentificationDataSource *p_identification_data_source)
   : _p_project(p_project)
 {
@@ -56,8 +55,7 @@ PepXmlSaxHandler::~PepXmlSaxHandler()
 
 bool
 PepXmlSaxHandler::startElement(const QString &namespaceURI,
-                               const QString &localName,
-                               const QString &qName,
+                               const QString &localName, const QString &qName,
                                const QXmlAttributes &attributes)
 {
   // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -130,9 +128,8 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in PepXmlSaxHandler::startElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::startElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -151,8 +148,7 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
 
 bool
 PepXmlSaxHandler::endElement(const QString &namespaceURI,
-                             const QString &localName,
-                             const QString &qName)
+                             const QString &localName, const QString &qName)
 {
 
   // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -175,9 +171,8 @@ PepXmlSaxHandler::endElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in PepXmlSaxHandler::endElement tag %1, "
-                    "PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::endElement tag %1, "
+                              "PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -309,10 +304,9 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
   if(attributes.value("retention_time_sec").isEmpty())
     {
       QString message =
-        QObject::tr(
-          "ERROR reading pepxml file :\n"
-          "unable to read search results from '%1' as retention time "
-          "is not given in spectrum_query elements")
+        QObject::tr("ERROR reading pepxml file :\n"
+                    "unable to read search results from '%1' as retention time "
+                    "is not given in spectrum_query elements")
           .arg(_current_search_engine);
       qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
                << message;
@@ -332,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
 
 //<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
 //       ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-//                                                 \
+//                                                  \
 //S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
 // peptide_next_aa="N"/>
 bool
@@ -696,9 +690,8 @@ PepXmlSaxHandler::endElement_modification_info()
 bool
 PepXmlSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -710,9 +703,8 @@ PepXmlSaxHandler::error(const QXmlParseException &exception)
 bool
 PepXmlSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
index ac42d0184e479eb90c0d39c4e73382a084704aeb..8856408c83d1c7cec5d1c68b4ff8b009174f1f18 100644
--- a/src/input/pepxmlsaxhandler.h
+++ b/src/input/pepxmlsaxhandler.h
@@ -46,13 +46,10 @@ class PepXmlSaxHandler : public QXmlDefaultHandler
                    IdentificationDataSource *p_identification_data_source);
   ~PepXmlSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 275cc3d1d9121b11c105dc4f1322bc99dbc035bc..603ed25d58334aab2de0e9e32b581196d1bca93b 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -50,8 +50,7 @@ XpipSaxHandler::isJavaXpip() const
 
 bool
 XpipSaxHandler::startElement(const QString &namespaceURI,
-                             const QString &localName,
-                             const QString &qName,
+                             const QString &localName, const QString &qName,
                              const QXmlAttributes &attributes)
 {
   qDebug() << "XpipSaxHandler::startElement begin" << namespaceURI << " "
@@ -138,8 +137,7 @@ XpipSaxHandler::startElement(const QString &namespaceURI,
 
 bool
 XpipSaxHandler::endElement(const QString &namespaceURI,
-                           const QString &localName,
-                           const QString &qName)
+                           const QString &localName, const QString &qName)
 {
 
   bool is_ok = true;
@@ -472,9 +470,8 @@ XpipSaxHandler::endElement_match()
 bool
 XpipSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -486,9 +483,8 @@ XpipSaxHandler::error(const QXmlParseException &exception)
 bool
 XpipSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index cc692ecd2c630c279acf064c25f988057fba1a26..4a4731c27345816c5e28809e3bdc743ed7cf3bc4 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -39,13 +39,10 @@ class XpipSaxHandler : public QXmlDefaultHandler
   XpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
   ~XpipSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/input/xtandemparamsaxhandler.cpp b/src/input/xtandemparamsaxhandler.cpp
index 3d0e2f4374df4e946ea7efeda58d88d2214d74ab..08b9feed0efd9aa3ac6fa1b0126c0fa6ed2a75e7 100644
--- a/src/input/xtandemparamsaxhandler.cpp
+++ b/src/input/xtandemparamsaxhandler.cpp
@@ -67,10 +67,10 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
         {
           if(qName != "bioml")
             {
-              _errorStr = QObject::tr(
-                            "ERROR in XtandemParamSaxHandler::startElement "
+              _errorStr =
+                QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
                             "root tag %1 is not <bioml>")
-                            .arg(qName);
+                  .arg(qName);
               return false;
             }
         }
@@ -84,18 +84,16 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemParamSaxHandler::startElement "
-                    "tag %1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+                              "tag %1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemParamSaxHandler::startElement "
-                    "tag %1, std exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+                              "tag %1, std exception:\n%2")
                     .arg(qName)
                     .arg(exception_std.what());
       return false;
@@ -121,18 +119,16 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemParamSaxHandler::endElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemParamSaxHandler::endElement tag "
-                    "%1, std exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
+                              "%1, std exception:\n%2")
                     .arg(qName)
                     .arg(exception_std.what());
       return false;
@@ -148,9 +144,8 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
 bool
 XtandemParamSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -162,9 +157,8 @@ XtandemParamSaxHandler::error(const QXmlParseException &exception)
 bool
 XtandemParamSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/xtandemparamsaxhandler.h b/src/input/xtandemparamsaxhandler.h
index f475174c9bdd5d15257c7ccd793d7e1b88c1b482..398f516ca4c03dd9551c99d7c9a6e5d7df30939f 100644
--- a/src/input/xtandemparamsaxhandler.h
+++ b/src/input/xtandemparamsaxhandler.h
@@ -41,13 +41,10 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
   XtandemParamSaxHandler(TandemParameters *p_tandem_parameters);
   ~XtandemParamSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 30df3c4a805b47e9fc26fbc87a25aa835b0289d7..57b17071e31ba50749e20ec2597256a1b0d68f92 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -40,8 +40,7 @@
 
 
 XtandemSaxHandler::XtandemSaxHandler(
-  Project *p_project,
-  IdentificationGroup *p_identification_group,
+  Project *p_project, IdentificationGroup *p_identification_group,
   IdentificationDataSource *p_identification_data_source)
   : _p_project(p_project)
 {
@@ -58,8 +57,7 @@ XtandemSaxHandler::~XtandemSaxHandler()
 
 bool
 XtandemSaxHandler::startElement(const QString &namespaceURI,
-                                const QString &localName,
-                                const QString &qName,
+                                const QString &localName, const QString &qName,
                                 const QXmlAttributes &attributes)
 {
   // qDebug() << namespaceURI << " " << localName << " " << qName ;
@@ -98,9 +96,8 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException &exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemSaxHandler::startElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -119,8 +116,7 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
 
 bool
 XtandemSaxHandler::endElement(const QString &namespaceURI,
-                              const QString &localName,
-                              const QString &qName)
+                              const QString &localName, const QString &qName)
 {
 
   bool is_ok = true;
@@ -142,9 +138,8 @@ XtandemSaxHandler::endElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException &exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtandemSaxHandler::endElement tag %1, "
-                    "PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, "
+                              "PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -224,10 +219,9 @@ XtandemSaxHandler::startElement_file(QXmlAttributes attributes)
       //                     attrs.getValue("URL")));
       if(_p_protein_match == nullptr)
         {
-          throw pappso::PappsoException(
-            "ERROR in "
-            "XtandemSaxHandler::startElement_file "
-            ": _p_protein_match == nullptr");
+          throw pappso::PappsoException("ERROR in "
+                                        "XtandemSaxHandler::startElement_file "
+                                        ": _p_protein_match == nullptr");
         }
       _p_protein_match->getProteinXtpSp().get()->setFastaFileP(
         _p_project->getFastaFileStore()
@@ -257,10 +251,9 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
       //""));
       if(_p_protein_match == nullptr)
         {
-          throw pappso::PappsoException(
-            "ERROR in "
-            "XtandemSaxHandler::startElement_"
-            "domain : _p_protein_match == nullptr");
+          throw pappso::PappsoException("ERROR in "
+                                        "XtandemSaxHandler::startElement_"
+                                        "domain : _p_protein_match == nullptr");
         }
 
       _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
@@ -422,10 +415,9 @@ XtandemSaxHandler::endElement_domain()
       .getInstance(_p_peptide_evidence));
   if(_p_protein_match == nullptr)
     {
-      throw pappso::PappsoException(
-        "ERROR in "
-        "XtandemSaxHandler::endElement_domain : "
-        "_p_protein_match == nullptr");
+      throw pappso::PappsoException("ERROR in "
+                                    "XtandemSaxHandler::endElement_domain : "
+                                    "_p_protein_match == nullptr");
     }
 
   _p_protein_match->addPeptideMatch(_current_peptide_match);
@@ -721,9 +713,8 @@ XtandemSaxHandler::endElement_note()
 bool
 XtandemSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -735,9 +726,8 @@ XtandemSaxHandler::error(const QXmlParseException &exception)
 bool
 XtandemSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index 75502f33fddeba4bf57174eb326761ad22f852fc..aa5bef914393fff6233b1a8225757724b35d384b 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/src/input/xtandemsaxhandler.h
@@ -49,13 +49,10 @@ class XtandemSaxHandler : public QXmlDefaultHandler
                     IdentificationDataSource *p_identification_data_source);
   ~XtandemSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 7c006d9f193888ddaf596a0c9cf55f4b574a3e34..d577fd393c8f94d1baf0ad5cd725c305c84f116a 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -58,8 +58,7 @@ XtpXpipSaxHandler::isXtpXpip() const
 }
 bool
 XtpXpipSaxHandler::startElement(const QString &namespaceURI,
-                                const QString &localName,
-                                const QString &qName,
+                                const QString &localName, const QString &qName,
                                 const QXmlAttributes &attributes)
 {
   qDebug() << "XtpXpipSaxHandler::startElement begin" << namespaceURI << " "
@@ -196,9 +195,8 @@ XtpXpipSaxHandler::startElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtpXpipSaxHandler::startElement tag "
-                    "%1, PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::startElement tag "
+                              "%1, PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -217,8 +215,7 @@ XtpXpipSaxHandler::startElement(const QString &namespaceURI,
 
 bool
 XtpXpipSaxHandler::endElement(const QString &namespaceURI,
-                              const QString &localName,
-                              const QString &qName)
+                              const QString &localName, const QString &qName)
 {
 
   qDebug() << "XtpXpipSaxHandler::endElement begin" << namespaceURI << " "
@@ -270,9 +267,8 @@ XtpXpipSaxHandler::endElement(const QString &namespaceURI,
     }
   catch(pappso::PappsoException exception_pappso)
     {
-      _errorStr = QObject::tr(
-                    "ERROR in XtpXpipSaxHandler::endElement tag %1, "
-                    "PAPPSO exception:\n%2")
+      _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::endElement tag %1, "
+                              "PAPPSO exception:\n%2")
                     .arg(qName)
                     .arg(exception_pappso.qwhat());
       return false;
@@ -868,9 +864,8 @@ XtpXpipSaxHandler::endElement_protein_match()
 bool
 XtpXpipSaxHandler::error(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
@@ -882,9 +877,8 @@ XtpXpipSaxHandler::error(const QXmlParseException &exception)
 bool
 XtpXpipSaxHandler::fatalError(const QXmlParseException &exception)
 {
-  _errorStr = QObject::tr(
-                "Parse error at line %1, column %2 :\n"
-                "%3")
+  _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                          "%3")
                 .arg(exception.lineNumber())
                 .arg(exception.columnNumber())
                 .arg(exception.message());
diff --git a/src/input/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index 1c595984d971894bac2b616513f53b7413aa2369..29f8767953cd2be02758081304c1080004e956a7 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -47,13 +47,10 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
   XtpXpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
   ~XtpXpipSaxHandler();
 
-  bool startElement(const QString &namespaceURI,
-                    const QString &localName,
-                    const QString &qName,
-                    const QXmlAttributes &attributes);
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
 
-  bool endElement(const QString &namespaceURI,
-                  const QString &localName,
+  bool endElement(const QString &namespaceURI, const QString &localName,
                   const QString &qName);
 
   bool startDocument();
diff --git a/src/output/exportfastafile.cpp b/src/output/exportfastafile.cpp
index b64e010fec677584358a8e41725d5e3731dde1a3..b7a424e068fddf2587d26d40a6c765a63a397ef1 100644
--- a/src/output/exportfastafile.cpp
+++ b/src/output/exportfastafile.cpp
@@ -79,8 +79,7 @@ ExportFastaFile::writeIdentificationGroup(
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getGroupingId() <
                          b->getGrpProteinSp().get()->getGroupingId();
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index c23754a28c9769af23f4e12bd76536d6c09d172f..1b0a9e404e1abd58b35c42d2977e8c293d6a0f4c 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -231,9 +231,8 @@ MassChroQml::writeQuantificationTraces()
   _output_stream->writeStartElement("quantification_traces");
   //<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
   //	format="tsv" />
-  _output_stream->writeComment(
-    "<peptide_traces peptide_ids=\"pep0 pep1\" "
-    "output_dir=\"pep_traces\" format=\"tsv\" />");
+  _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" "
+                               "output_dir=\"pep_traces\" format=\"tsv\" />");
   /*
       <all_xics_traces output_dir="all_xics_traces" format="tsv" />
       <mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
@@ -278,9 +277,8 @@ MassChroQml::writeQuantify()
     }
   _output_stream->writeEndElement();
 
-  _output_stream->writeComment(
-    "<mz_list>732.317 449.754 552.234 464.251 "
-    "381.577 569.771 575.256</mz_list>");
+  _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 "
+                               "381.577 569.771 575.256</mz_list>");
   _output_stream->writeComment(
     "<mzrt_list>\n				<mzrt mz=\"732.317\" rt=\"230.712\" />\n			<mzrt "
     "mz=\"575.256\" rt=\"254.788\" />\n			</mzrt_list>");
@@ -505,8 +503,7 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
     }
 
   // sort list
-  std::sort(mcq_peptide_list.begin(),
-            mcq_peptide_list.end(),
+  std::sort(mcq_peptide_list.begin(), mcq_peptide_list.end(),
             [](const McqPeptide &first, const McqPeptide &second) {
               return (first.id < second.id);
             });
@@ -592,8 +589,7 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
         }
 
       //<observed_in data="samp0" scan="655" z="2" />
-      std::sort(mcq_peptide.observed_in.begin(),
-                mcq_peptide.observed_in.end(),
+      std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),
                 [](const McqObserved &first, const McqObserved &second) {
                   return std::tie(first.charge, first.scan, first.msrun) <
                          std::tie(second.charge, second.scan, second.msrun);
diff --git a/src/output/mcqr/mcqrscpeptide.cpp b/src/output/mcqr/mcqrscpeptide.cpp
index 8d9bca9bd6982f71d1b9ad9a355925b4c3477d0d..a855c9dd6f5899ce94e8ce837c2f59a9d98b8978 100644
--- a/src/output/mcqr/mcqrscpeptide.cpp
+++ b/src/output/mcqr/mcqrscpeptide.cpp
@@ -98,8 +98,7 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getSubGroupNumber() <
                          b->getGrpProteinSp().get()->getSubGroupNumber();
@@ -126,10 +125,8 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
               std::vector<PeptideMatch> peptide_match_in_msrun =
                 protein_match->getPeptideMatchList(validation_state,
                                                    msrun_sp.get());
-              writePeptidesInMsrun(protein_match,
-                                   msrun_sp.get(),
-                                   peptide_match_in_msrun,
-                                   count_scan_zero);
+              writePeptidesInMsrun(protein_match, msrun_sp.get(),
+                                   peptide_match_in_msrun, count_scan_zero);
             }
         }
     }
@@ -139,8 +136,7 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
 
 void
 McqRscPeptide::writePeptidesInMsrun(
-  const ProteinMatch *p_protein_match,
-  const MsRun *p_msrun,
+  const ProteinMatch *p_protein_match, const MsRun *p_msrun,
   const std::vector<PeptideMatch> &peptide_match_in_msrun,
   const std::map<ScPeptideLabel, std::size_t> &count_scan_zero)
 {
@@ -198,8 +194,7 @@ McqRscPeptide::writePeptidesInMsrun(
             (unsigned int)p_protein_match->getGroupingGroupSp()
               .get()
               ->countSpecificSequenceLi(p_protein_match,
-                                        ValidationState::grouped,
-                                        p_msrun,
+                                        ValidationState::grouped, p_msrun,
                                         pair_count.first._p_label));
         }
       qDebug() << "McqRscPeptide::writePeptidesInMsrun end";
diff --git a/src/output/mcqr/mcqrscpeptide.h b/src/output/mcqr/mcqrscpeptide.h
index 76984f839e94d385041253fa6e4a3df75f511f3c..977a478fe17f0256b2e8449a19482b9a17b26dc9 100644
--- a/src/output/mcqr/mcqrscpeptide.h
+++ b/src/output/mcqr/mcqrscpeptide.h
@@ -55,8 +55,7 @@ class McqRscPeptide
   void writeIdentificationGroup(IdentificationGroup *p_ident);
   void writeHeaders(IdentificationGroup *p_ident);
   void writePeptidesInMsrun(
-    const ProteinMatch *p_protein_match,
-    const MsRun *p_msrun,
+    const ProteinMatch *p_protein_match, const MsRun *p_msrun,
     const std::vector<PeptideMatch> &peptide_match_in_msrun,
     const std::map<ScPeptideLabel, std::size_t> &count_scan_zero);
 
diff --git a/src/output/mcqr/mcqrscprotein.cpp b/src/output/mcqr/mcqrscprotein.cpp
index c6c34ce3c8212c6d5707f275f5364d16755e58ce..b77b4830c2fe473ac7351abeb13bdd746bd55c36 100644
--- a/src/output/mcqr/mcqrscprotein.cpp
+++ b/src/output/mcqr/mcqrscprotein.cpp
@@ -87,8 +87,7 @@ McqRscProtein::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getSubGroupNumber() <
                          b->getGrpProteinSp().get()->getSubGroupNumber();
diff --git a/src/output/mcqrspectralcount.cpp b/src/output/mcqrspectralcount.cpp
index 7821a23b0b98086a89ebe1ee4b90b611586f7d03..5f0346f4975e38205aab3bd6f1c7fdda2f771bac 100644
--- a/src/output/mcqrspectralcount.cpp
+++ b/src/output/mcqrspectralcount.cpp
@@ -102,8 +102,7 @@ McqrSpectralCount::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getSubGroupNumber() <
                          b->getGrpProteinSp().get()->getSubGroupNumber();
@@ -140,21 +139,15 @@ McqrSpectralCount::writeOneProtein(const GroupingGroup *p_group,
 
           if(_label_list.size() == 0)
             {
-              writeOneProteinLabel(p_grp_protein,
-                                   msrun_sp.get(),
-                                   nullptr,
-                                   p_protein,
-                                   p_protein_match);
+              writeOneProteinLabel(p_grp_protein, msrun_sp.get(), nullptr,
+                                   p_protein, p_protein_match);
             }
           else
             {
               for(auto &p_label : _label_list)
                 {
-                  writeOneProteinLabel(p_grp_protein,
-                                       msrun_sp.get(),
-                                       p_label,
-                                       p_protein,
-                                       p_protein_match);
+                  writeOneProteinLabel(p_grp_protein, msrun_sp.get(), p_label,
+                                       p_protein, p_protein_match);
                 }
             }
         }
@@ -201,9 +194,9 @@ McqrSpectralCount::writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
   _p_writer->writeCell(p_protein_match->countSampleScan(
     ValidationState::grouped, p_msrun, p_label));
 
-  _p_writer->writeCell(
-    (unsigned int)p_protein_match->getGroupingGroupSp()
-      .get()
-      ->countSpecificSampleScan(
-        p_protein_match, ValidationState::grouped, p_msrun, p_label));
+  _p_writer->writeCell((unsigned int)p_protein_match->getGroupingGroupSp()
+                         .get()
+                         ->countSpecificSampleScan(p_protein_match,
+                                                   ValidationState::grouped,
+                                                   p_msrun, p_label));
 }
diff --git a/src/output/mcqrspectralcount.h b/src/output/mcqrspectralcount.h
index d6a401335eb95da8519e77c5d3aa90e1f4de6b3d..bf26cfd836bb8eb8bd5ebb37f08c5ad7b4c5fc73 100644
--- a/src/output/mcqrspectralcount.h
+++ b/src/output/mcqrspectralcount.h
@@ -47,8 +47,7 @@ class McqrSpectralCount
   void writeOneProtein(const GroupingGroup *p_group,
                        const ProteinMatch *p_protein_match);
   void writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
-                            const MsRun *p_msrun,
-                            const Label *p_label,
+                            const MsRun *p_msrun, const Label *p_label,
                             const ProteinXtp *p_protein,
                             const ProteinMatch *p_protein_match);
 
diff --git a/src/output/ods/comparbasesheet.cpp b/src/output/ods/comparbasesheet.cpp
index 3c7bfaa5533bc635701407f3559d173a051862d2..88e1115b2fe45d9f613207a81d6ab34f595388f2 100644
--- a/src/output/ods/comparbasesheet.cpp
+++ b/src/output/ods/comparbasesheet.cpp
@@ -164,8 +164,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
     {
       if(_label_list.size() == 0)
         {
-          writeComparValue(
-            p_protein_match, ValidationState::validAndChecked, msrun_sp.get());
+          writeComparValue(p_protein_match, ValidationState::validAndChecked,
+                           msrun_sp.get());
           if(_first_cell_coordinate.isEmpty())
             {
               _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
@@ -176,8 +176,7 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
           for(const Label *p_label : _label_list)
             {
               writeComparValue(p_protein_match,
-                               ValidationState::validAndChecked,
-                               msrun_sp.get(),
+                               ValidationState::validAndChecked, msrun_sp.get(),
                                p_label);
               if(_first_cell_coordinate.isEmpty())
                 {
@@ -212,8 +211,7 @@ ComparBaseSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
     }
 
   std::sort(
-    protein_match_list.begin(),
-    protein_match_list.end(),
+    protein_match_list.begin(), protein_match_list.end(),
     [](const ProteinMatch *a, const ProteinMatch *b) {
       unsigned int agroup    = a->getGrpProteinSp().get()->getGroupNumber();
       unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
diff --git a/src/output/ods/comparbasesheet.h b/src/output/ods/comparbasesheet.h
index c5871f865a1172fcbd0e8cdaea2f9e34a2085d0c..4b85ab7d9fc2fb5a9a8468c4045902cf362d549e 100644
--- a/src/output/ods/comparbasesheet.h
+++ b/src/output/ods/comparbasesheet.h
@@ -39,8 +39,7 @@
 class ComparBaseSheet
 {
   public:
-  ComparBaseSheet(OdsExport *p_ods_export,
-                  CalcWriterInterface *p_writer,
+  ComparBaseSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   private:
@@ -52,8 +51,7 @@ class ComparBaseSheet
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) = 0;
   void writeProteinMatch(const ProteinMatch *p_protein_match);
 
diff --git a/src/output/ods/comparspecificspectrasheet.cpp b/src/output/ods/comparspecificspectrasheet.cpp
index 20e6923abcd678101b7fad94f5de2f67f3f126c3..5ad6c4fed7af0d0536b79ce0d2d255916fdc3cc3 100644
--- a/src/output/ods/comparspecificspectrasheet.cpp
+++ b/src/output/ods/comparspecificspectrasheet.cpp
@@ -32,8 +32,7 @@
 
 
 ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
-  OdsExport *p_ods_export,
-  CalcWriterInterface *p_writer,
+  OdsExport *p_ods_export, CalcWriterInterface *p_writer,
   const Project *p_project)
   : ComparBaseSheet(p_ods_export, p_writer, p_project)
 {
@@ -43,10 +42,8 @@ ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
 
 void
 ComparSpecificSpectraSheet::writeComparValue(
-  const ProteinMatch *p_protein_match,
-  ValidationState state,
-  const MsRun *p_msrun,
-  const Label *p_label)
+  const ProteinMatch *p_protein_match, ValidationState state,
+  const MsRun *p_msrun, const Label *p_label)
 {
   qDebug() << "ComparSpecificSpectraSheet::writeComparValue begin";
   _p_writer->writeCell(
@@ -58,8 +55,7 @@ ComparSpecificSpectraSheet::writeComparValue(
 
 
 ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
-  OdsExport *p_ods_export,
-  CalcWriterInterface *p_writer,
+  OdsExport *p_ods_export, CalcWriterInterface *p_writer,
   const Project *p_project)
   : ComparBaseSheet(p_ods_export, p_writer, p_project)
 {
@@ -68,10 +64,8 @@ ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
 
 void
 ComparSpecificSequenceSheet::writeComparValue(
-  const ProteinMatch *p_protein_match,
-  ValidationState state,
-  const MsRun *p_msrun,
-  const Label *p_label)
+  const ProteinMatch *p_protein_match, ValidationState state,
+  const MsRun *p_msrun, const Label *p_label)
 {
   qDebug() << "ComparSpecificSequenceSheet::writeComparValue begin";
   _p_writer->writeCell(
diff --git a/src/output/ods/comparspecificspectrasheet.h b/src/output/ods/comparspecificspectrasheet.h
index e677f28f97ffcfd02bff8684b364b2979082220e..90398835876a79e96aff937a41e534b01402e724 100644
--- a/src/output/ods/comparspecificspectrasheet.h
+++ b/src/output/ods/comparspecificspectrasheet.h
@@ -41,8 +41,7 @@ class ComparSpecificSpectraSheet : public ComparBaseSheet
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
@@ -55,8 +54,7 @@ class ComparSpecificSequenceSheet : public ComparBaseSheet
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
diff --git a/src/output/ods/comparspectrabypeptide.cpp b/src/output/ods/comparspectrabypeptide.cpp
index 2898bbe1dc4ebae75ac3dd548363f8ab80b76e14..1649ee15b700fb22a73b112feef2168f867b67bc 100644
--- a/src/output/ods/comparspectrabypeptide.cpp
+++ b/src/output/ods/comparspectrabypeptide.cpp
@@ -132,8 +132,7 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const PeptideEvidence *> peptide_evidence_list =
         group_pair.second.get()->getPeptideEvidenceList();
 
-      std::sort(peptide_evidence_list.begin(),
-                peptide_evidence_list.end(),
+      std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
                 [](const PeptideEvidence *a, const PeptideEvidence *b) {
                   return a->getGrpPeptideSp().get()->getRank() <
                          b->getGrpPeptideSp().get()->getRank();
@@ -199,8 +198,8 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
 
       if(p_best_peptide_evidence != nullptr)
         {
-          writeBestPeptideEvidence(
-            group_pair.second.get(), p_best_peptide_evidence, sample_scan_list);
+          writeBestPeptideEvidence(group_pair.second.get(),
+                                   p_best_peptide_evidence, sample_scan_list);
           sample_scan_list.clear();
         }
     }
@@ -222,8 +221,7 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
 
 void
 ComparSpectraByPeptide::writeBestPeptideEvidence(
-  const GroupingGroup *p_group,
-  const PeptideEvidence *p_peptide_evidence,
+  const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence,
   const std::map<QString, std::vector<size_t>> &sample_scan_list)
 {
 
@@ -257,8 +255,8 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
     {
       if(_label_list.size() == 0)
         {
-          writeComparValue(
-            sample_scan_list, ValidationState::validAndChecked, msrun_sp.get());
+          writeComparValue(sample_scan_list, ValidationState::validAndChecked,
+                           msrun_sp.get());
           if(_first_cell_coordinate.isEmpty())
             {
               _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
@@ -269,8 +267,7 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
           for(const Label *p_label : _label_list)
             {
               writeComparValue(sample_scan_list,
-                               ValidationState::validAndChecked,
-                               msrun_sp.get(),
+                               ValidationState::validAndChecked, msrun_sp.get(),
                                p_label);
               if(_first_cell_coordinate.isEmpty())
                 {
@@ -285,9 +282,7 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
 void
 ComparSpectraByPeptide::writeComparValue(
   const std::map<QString, std::vector<size_t>> &sample_scan_list,
-  ValidationState state,
-  const MsRun *p_msrun,
-  const Label *p_label)
+  ValidationState state, const MsRun *p_msrun, const Label *p_label)
 {
   /*
   std::sort(sample_scan_list.begin(), sample_scan_list.end());
diff --git a/src/output/ods/comparspectrabypeptide.h b/src/output/ods/comparspectrabypeptide.h
index a566384d31c783fc0b29ce3dd4a9c0d3a23d446a..97436247ff6f6ccffd05737e6d985cae666cc8f1 100644
--- a/src/output/ods/comparspectrabypeptide.h
+++ b/src/output/ods/comparspectrabypeptide.h
@@ -50,18 +50,15 @@ class ComparSpectraByPeptide
   void writeIdentificationGroup(IdentificationGroup *p_ident);
   void writeHeaders(IdentificationGroup *p_ident);
   void writeBestPeptideEvidence(
-    const GroupingGroup *p_group,
-    const PeptideEvidence *p_peptide_evidence,
+    const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence,
     const std::map<QString, std::vector<size_t>> &sample_scan_list);
   void writeComparValue(
     const std::map<QString, std::vector<size_t>> &sample_scan_list,
-    ValidationState state,
-    const MsRun *p_msrun,
+    ValidationState state, const MsRun *p_msrun,
     const Label *p_label = nullptr);
 
   public:
-  ComparSpectraByPeptide(OdsExport *p_ods_export,
-                         CalcWriterInterface *p_writer,
+  ComparSpectraByPeptide(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                          const Project *p_project);
   void writeSheet();
 };
diff --git a/src/output/ods/comparspectrasheet.cpp b/src/output/ods/comparspectrasheet.cpp
index b9ee4cc32c6eb1f6d0e503358be87e0935e9f503..184ee49aa09b619373c9c131235be981ba6236a9 100644
--- a/src/output/ods/comparspectrasheet.cpp
+++ b/src/output/ods/comparspectrasheet.cpp
@@ -46,8 +46,7 @@ ComparSpectraSheet::ComparSpectraSheet(OdsExport *p_ods_export,
 void
 ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
                                      ValidationState state,
-                                     const MsRun *p_msrun,
-                                     const Label *p_label)
+                                     const MsRun *p_msrun, const Label *p_label)
 {
   qDebug() << "ComparSpectraSheet::writeComparValue begin";
   _p_writer->writeCell(
@@ -86,8 +85,7 @@ ComparPaiSheet::ComparPaiSheet(OdsExport *p_ods_export,
 
 void
 ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                 ValidationState state,
-                                 const MsRun *p_msrun,
+                                 ValidationState state, const MsRun *p_msrun,
                                  const Label *p_label)
 {
   qDebug() << "ComparPaiSheet::writeComparValue begin";
@@ -105,8 +103,7 @@ ComparEmpaiSheet::ComparEmpaiSheet(OdsExport *p_ods_export,
 
 void
 ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                   ValidationState state,
-                                   const MsRun *p_msrun,
+                                   ValidationState state, const MsRun *p_msrun,
                                    const Label *p_label)
 {
   qDebug() << "ComparEmpaiSheet::writeComparValue begin";
@@ -124,8 +121,7 @@ ComparNsafSheet::ComparNsafSheet(OdsExport *p_ods_export,
 
 void
 ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                  ValidationState state,
-                                  const MsRun *p_msrun,
+                                  ValidationState state, const MsRun *p_msrun,
                                   const Label *p_label)
 {
   qDebug() << "ComparNsafSheet::writeComparValue begin";
diff --git a/src/output/ods/comparspectrasheet.h b/src/output/ods/comparspectrasheet.h
index d129f71f728bd408dc887d27843dbf7720014a28..04b0df804e5d026985c24b9eab7e3b7372fac212 100644
--- a/src/output/ods/comparspectrasheet.h
+++ b/src/output/ods/comparspectrasheet.h
@@ -36,14 +36,12 @@
 class ComparSpectraSheet : public ComparBaseSheet
 {
   public:
-  ComparSpectraSheet(OdsExport *p_ods_export,
-                     CalcWriterInterface *p_writer,
+  ComparSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                      const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
@@ -51,56 +49,48 @@ class ComparSpectraSheet : public ComparBaseSheet
 class ComparSequenceSheet : public ComparBaseSheet
 {
   public:
-  ComparSequenceSheet(OdsExport *p_ods_export,
-                      CalcWriterInterface *p_writer,
+  ComparSequenceSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                       const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
 class ComparPaiSheet : public ComparBaseSheet
 {
   public:
-  ComparPaiSheet(OdsExport *p_ods_export,
-                 CalcWriterInterface *p_writer,
+  ComparPaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                  const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
 class ComparEmpaiSheet : public ComparBaseSheet
 {
   public:
-  ComparEmpaiSheet(OdsExport *p_ods_export,
-                   CalcWriterInterface *p_writer,
+  ComparEmpaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                    const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 };
 
 class ComparNsafSheet : public ComparBaseSheet
 {
   public:
-  ComparNsafSheet(OdsExport *p_ods_export,
-                  CalcWriterInterface *p_writer,
+  ComparNsafSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
-                                ValidationState state,
-                                const MsRun *p_msrun,
+                                ValidationState state, const MsRun *p_msrun,
                                 const Label *p_label = nullptr) override;
 
   private:
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
index 524e37dc6eefd0fa094e1cc672ec04c9706fe0d8..1842d454c34845aab09630b2dbe8fcc6dca02a47 100644
--- a/src/output/ods/groupingsheet.cpp
+++ b/src/output/ods/groupingsheet.cpp
@@ -105,9 +105,8 @@ GroupingSheet::writeHeaders()
     "identification engine");
   _p_writer->writeCell("psm");
   //_p_writer->writeCell("sequences");
-  _p_writer->setCellAnnotation(
-    "number of unique combinations : grouped "
-    "peptide sequence+modifications+sample name");
+  _p_writer->setCellAnnotation("number of unique combinations : grouped "
+                               "peptide sequence+modifications+sample name");
   _p_writer->writeCell("peptide/mass/sample");
   _p_writer->setCellAnnotation(
     "FDR at the protein level (number of decoy valid proteins / total number "
diff --git a/src/output/ods/groupingsheet.h b/src/output/ods/groupingsheet.h
index ec253be645b5bcc650fd78ef45d4639903479aa3..9202bc4fd7b64a0bcebd3537502c0ea891849218 100644
--- a/src/output/ods/groupingsheet.h
+++ b/src/output/ods/groupingsheet.h
@@ -38,8 +38,7 @@
 class GroupingSheet
 {
   public:
-  GroupingSheet(OdsExport *p_ods_export,
-                CalcWriterInterface *p_writer,
+  GroupingSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                 const Project *p_project);
 
   private:
diff --git a/src/output/ods/infosheet.cpp b/src/output/ods/infosheet.cpp
index 4b6699e6fc1d5d08631611dd0c6de70c89b471c7..364bacfbaea13c6a3419de8d84fe951274c3614a 100644
--- a/src/output/ods/infosheet.cpp
+++ b/src/output/ods/infosheet.cpp
@@ -34,8 +34,7 @@
 #include <QSettings>
 
 
-InfoSheet::InfoSheet(OdsExport *p_ods_export,
-                     CalcWriterInterface *p_writer,
+InfoSheet::InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                      const Project *p_project)
   : _p_project(p_project)
 {
@@ -130,9 +129,8 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export,
   if(settings.value("export_ods/groups", "true").toBool())
     {
       p_writer->writeCell("groups");
-      p_writer->writeCell(
-        "simple statistics on the current grouping "
-        "experiment (numbers of groups, subgroups...)");
+      p_writer->writeCell("simple statistics on the current grouping "
+                          "experiment (numbers of groups, subgroups...)");
       p_writer->writeLine();
     }
 
@@ -146,29 +144,26 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export,
   if(settings.value("export_ods/peptides", "true").toBool())
     {
       p_writer->writeCell("peptides");
-      p_writer->writeCell(
-        "list of peptides used by the grouping algorithm. "
-        "Beware : peptides are intended as unique pairs of "
-        "sequence+mass, given that Leucine and Isoleucine as "
-        "the same mass, all Leucines are considered as "
-        "Isoleucines");
+      p_writer->writeCell("list of peptides used by the grouping algorithm. "
+                          "Beware : peptides are intended as unique pairs of "
+                          "sequence+mass, given that Leucine and Isoleucine as "
+                          "the same mass, all Leucines are considered as "
+                          "Isoleucines");
       p_writer->writeLine();
     }
   if(settings.value("export_ods/spectra", "true").toBool())
     {
       p_writer->writeCell("spectra");
-      p_writer->writeCell(
-        "list of all validated and checked spectrum match. "
-        "Only the best assigned peptide (best Evalue) is "
-        "reported ");
+      p_writer->writeCell("list of all validated and checked spectrum match. "
+                          "Only the best assigned peptide (best Evalue) is "
+                          "reported ");
       p_writer->writeLine();
     }
   if(settings.value("export_ods/peptidepos", "true").toBool())
     {
       p_writer->writeCell("peptide pos");
-      p_writer->writeCell(
-        "list of all *real* peptides identified on their "
-        "proteins, with their position on the sequence.");
+      p_writer->writeCell("list of all *real* peptides identified on their "
+                          "proteins, with their position on the sequence.");
       p_writer->writeLine();
     }
 }
diff --git a/src/output/ods/infosheet.h b/src/output/ods/infosheet.h
index c85a4f673a2ef23d623fbc30e4417ef62d759fe5..e3ec4d4200dc6ff9ebbca015bf0989fd05f5fd13 100644
--- a/src/output/ods/infosheet.h
+++ b/src/output/ods/infosheet.h
@@ -39,8 +39,7 @@
 class InfoSheet
 {
   public:
-  InfoSheet(OdsExport *p_ods_export,
-            CalcWriterInterface *p_writer,
+  InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
             const Project *p_project);
 
   private:
diff --git a/src/output/ods/peptidepossheet.cpp b/src/output/ods/peptidepossheet.cpp
index e3e8596270bc034900d57ba99cecb5ad216f59be..9918513ab2ae6008b353b0a3e6410612ee4c1a42 100644
--- a/src/output/ods/peptidepossheet.cpp
+++ b/src/output/ods/peptidepossheet.cpp
@@ -149,8 +149,7 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
     }
 
   std::sort(
-    protein_match_list.begin(),
-    protein_match_list.end(),
+    protein_match_list.begin(), protein_match_list.end(),
     [](const ProteinMatch *a, const ProteinMatch *b) {
       unsigned int agroup    = a->getGrpProteinSp().get()->getGroupNumber();
       unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
@@ -175,8 +174,7 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
             continue;
           peptide_match_list.push_back(peptide_match);
         }
-      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) {
                   unsigned int arank =
                     a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
diff --git a/src/output/ods/peptidepossheet.h b/src/output/ods/peptidepossheet.h
index d65740fd43f14c86f17c503aca23623be33003ba..a7b32bf8cfc34ea6a970f7abc372fb21d37ceaf1 100644
--- a/src/output/ods/peptidepossheet.h
+++ b/src/output/ods/peptidepossheet.h
@@ -41,8 +41,7 @@
 class PeptidePosSheet
 {
   public:
-  PeptidePosSheet(OdsExport *p_ods_export,
-                  CalcWriterInterface *p_writer,
+  PeptidePosSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   private:
diff --git a/src/output/ods/peptidesheet.cpp b/src/output/ods/peptidesheet.cpp
index c05710d44f9ada89362610a91384a4686565dfc7..8e97e737a2595d7b615f4c63f3d716ff3c37e5a1 100644
--- a/src/output/ods/peptidesheet.cpp
+++ b/src/output/ods/peptidesheet.cpp
@@ -101,8 +101,7 @@ PeptideSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const PeptideEvidence *> peptide_evidence_list =
         group_pair.second.get()->getPeptideEvidenceList();
 
-      std::sort(peptide_evidence_list.begin(),
-                peptide_evidence_list.end(),
+      std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
                 [](const PeptideEvidence *a, const PeptideEvidence *b) {
                   return a->getGrpPeptideSp().get()->getRank() <
                          b->getGrpPeptideSp().get()->getRank();
diff --git a/src/output/ods/peptidesheet.h b/src/output/ods/peptidesheet.h
index 1f64c4bed11563c7ab16aef1439b7db6dd8881e8..7db49c459755b1ee2c01ea27459fa19d643ae125 100644
--- a/src/output/ods/peptidesheet.h
+++ b/src/output/ods/peptidesheet.h
@@ -39,8 +39,7 @@
 class PeptideSheet
 {
   public:
-  PeptideSheet(OdsExport *p_ods_export,
-               CalcWriterInterface *p_writer,
+  PeptideSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                const Project *p_project);
 
   private:
diff --git a/src/output/ods/proteinsheet.cpp b/src/output/ods/proteinsheet.cpp
index 90a6d82e4dbabf545ecaf66f4c95d33e2a8abe8f..70fc14d52dc9e2f845dfa35bcca583a9dfd809e5 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -141,8 +141,7 @@ ProteinSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getGroupingId() <
                          b->getGrpProteinSp().get()->getGroupingId();
diff --git a/src/output/ods/proteinsheet.h b/src/output/ods/proteinsheet.h
index a4e7347af2df7070152aa3a9e2fc2cab6f1b9d13..660256246b3d3b08c939b7cf6d86dbcb038d87bc 100644
--- a/src/output/ods/proteinsheet.h
+++ b/src/output/ods/proteinsheet.h
@@ -40,8 +40,7 @@
 class ProteinSheet
 {
   public:
-  ProteinSheet(OdsExport *p_ods_export,
-               CalcWriterInterface *p_writer,
+  ProteinSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                const Project *p_project);
 
   private:
diff --git a/src/output/ods/ptm/ptmislandsheet.cpp b/src/output/ods/ptm/ptmislandsheet.cpp
index e6d9489f00d53cf0446998849266ad2ad59fba4f..87e15abec5abe9bbeb629eccf985a0ec6653b33c 100644
--- a/src/output/ods/ptm/ptmislandsheet.cpp
+++ b/src/output/ods/ptm/ptmislandsheet.cpp
@@ -133,8 +133,7 @@ PtmIslandSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
       ptm_island_list.push_back(ptm_island_sp);
     }
   qDebug() << "PtmIslandSheet::writeIdentificationGroup sort";
-  std::sort(ptm_island_list.begin(),
-            ptm_island_list.end(),
+  std::sort(ptm_island_list.begin(), ptm_island_list.end(),
             [](PtmIslandSp &a, PtmIslandSp &b) {
               return a.get()->getGroupingId() < b.get()->getGroupingId();
             });
diff --git a/src/output/ods/ptm/ptmislandsheet.h b/src/output/ods/ptm/ptmislandsheet.h
index dcf46ad298193be515b7f28836a67feed59169d2..b9e9071fd792d0f03e6d77670e9c0efd38cdf9f8 100644
--- a/src/output/ods/ptm/ptmislandsheet.h
+++ b/src/output/ods/ptm/ptmislandsheet.h
@@ -40,8 +40,7 @@
 class PtmIslandSheet
 {
   public:
-  PtmIslandSheet(OdsExport *p_ods_export,
-                 CalcWriterInterface *p_writer,
+  PtmIslandSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                  const Project *p_project);
 
   private:
diff --git a/src/output/ods/ptm/ptmspectrasheet.h b/src/output/ods/ptm/ptmspectrasheet.h
index 4832ebeebbc7118d8ae38ac7e27e5f247435999c..6b589c045e6ee0e065899167e3416511a66a29ed 100644
--- a/src/output/ods/ptm/ptmspectrasheet.h
+++ b/src/output/ods/ptm/ptmspectrasheet.h
@@ -40,15 +40,12 @@
 class PtmSpectraSheet
 {
   public:
-  PtmSpectraSheet(OdsExport *p_ods_export,
-                  CalcWriterInterface *p_writer,
+  PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   protected:
-  PtmSpectraSheet(OdsExport *p_ods_export,
-                  CalcWriterInterface *p_writer,
-                  const Project *p_project,
-                  const QString &sheet_name);
+  PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+                  const Project *p_project, const QString &sheet_name);
   virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
   void writeHeaders(IdentificationGroup *p_ident);
   void writeBestPeptideEvidence(
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index a3c78b2a6b07ad7bad8f2635782a0a113af224f5..5fe39259fef811b24b10052bfca30773d09984b2 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -30,8 +30,7 @@
 
 #include "samplesheet.h"
 
-SampleSheet::SampleSheet(OdsExport *p_ods_export,
-                         CalcWriterInterface *p_writer,
+SampleSheet::SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                          const Project *p_project)
   : _p_project(p_project)
 {
@@ -119,19 +118,16 @@ SampleSheet::writeHeaders()
         "total number of MS level 3 during the MS run (from mz file)");
       _p_writer->writeCell("Total MS3");
 
-      _p_writer->setCellAnnotation(
-        "total ion current in MS level 1 spectra "
-        "during the MS run (from mz file)");
+      _p_writer->setCellAnnotation("total ion current in MS level 1 spectra "
+                                   "during the MS run (from mz file)");
       _p_writer->writeCell("TIC MS1");
 
-      _p_writer->setCellAnnotation(
-        "total ion current in MS level 2 spectra "
-        "during the MS run (from mz file)");
+      _p_writer->setCellAnnotation("total ion current in MS level 2 spectra "
+                                   "during the MS run (from mz file)");
       _p_writer->writeCell("TIC MS2");
 
-      _p_writer->setCellAnnotation(
-        "total ion current in MS level 3 spectra "
-        "during the MS run (from mz file)");
+      _p_writer->setCellAnnotation("total ion current in MS level 3 spectra "
+                                   "during the MS run (from mz file)");
       _p_writer->writeCell("TIC MS3");
     }
 
diff --git a/src/output/ods/samplesheet.h b/src/output/ods/samplesheet.h
index ce0181945787a6fc4c76e43b0eb449ed512128f6..12677f5f2186c78196fda60434185f57c15b0f59 100644
--- a/src/output/ods/samplesheet.h
+++ b/src/output/ods/samplesheet.h
@@ -38,8 +38,7 @@
 class SampleSheet
 {
   public:
-  SampleSheet(OdsExport *p_ods_export,
-              CalcWriterInterface *p_writer,
+  SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
               const Project *p_project);
 
   private:
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index 4fc18127664d0dacd023f598fcc6490952160d5d..c260028ca98c9eac00e4a481c81d0993079512d5 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -34,8 +34,7 @@
 
 SpectraSheet::SpectraSheet(OdsExport *p_ods_export,
                            CalcWriterInterface *p_writer,
-                           const Project *p_project,
-                           const QString &sheet_name)
+                           const Project *p_project, const QString &sheet_name)
   : _p_project(p_project)
 {
   _p_ods_export = p_ods_export;
@@ -176,8 +175,7 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
         group_pair.second.get()->getPeptideEvidenceList();
 
       std::sort(
-        peptide_evidence_list.begin(),
-        peptide_evidence_list.end(),
+        peptide_evidence_list.begin(), peptide_evidence_list.end(),
         [](const PeptideEvidence *a, const PeptideEvidence *b) {
           unsigned int arank = a->getGrpPeptideSp().get()->getRank();
           unsigned int ascan = a->getScan();
@@ -206,8 +204,8 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
           if(std::tie(arank,
                       p_best_peptide_evidence->getMsRunP()->getSampleName(),
                       ascan) !=
-             std::tie(
-               brank, peptide_evidence->getMsRunP()->getSampleName(), bscan))
+             std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(),
+                      bscan))
             {
               // write p_best_peptide_match
               writeBestPeptideEvidence(group_pair.second.get(),
diff --git a/src/output/ods/spectrasheet.h b/src/output/ods/spectrasheet.h
index afbecc2c1a233f6ccda314839140a7cf1bb682c2..5035d45aed2ce9f09695a7d67b70fa3c7d4dc20c 100644
--- a/src/output/ods/spectrasheet.h
+++ b/src/output/ods/spectrasheet.h
@@ -40,15 +40,12 @@
 class SpectraSheet
 {
   public:
-  SpectraSheet(OdsExport *p_ods_export,
-               CalcWriterInterface *p_writer,
+  SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
                const Project *p_project);
 
   protected:
-  SpectraSheet(OdsExport *p_ods_export,
-               CalcWriterInterface *p_writer,
-               const Project *p_project,
-               const QString &sheet_name);
+  SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+               const Project *p_project, const QString &sheet_name);
   virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
   void writeHeaders(IdentificationGroup *p_ident);
   void writeBestPeptideEvidence(const GroupingGroup *p_group,
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 8e08e19f9073bdeab8704d7203ec311fcfa42eb0..1542d45461f7561d1ef53e43fce04bf0d76d4ddb 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -542,8 +542,7 @@ ProticdbMl::writepeptideHitsbyGroup(GroupingGroup *p_group)
           protic_peptide_hit_list.push_back(protic_peptide_hit);
         }
     }
-  std::sort(protic_peptide_hit_list.begin(),
-            protic_peptide_hit_list.end(),
+  std::sort(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end(),
             [](const ProticPeptideHit &first, const ProticPeptideHit &second) {
               return (first.key < second.key);
             });
@@ -616,10 +615,9 @@ ProticdbMl::writePeptideHit(QString xml_id,
       protic_peptide_hit.peptide_match.getPeptideEvidence()->getScan()));
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   _output_stream->writeAttribute(
-    "ms_run_id",
-    protic_peptide_hit.peptide_match.getPeptideEvidence()
-      ->getMsRunP()
-      ->getXmlId());
+    "ms_run_id", protic_peptide_hit.peptide_match.getPeptideEvidence()
+                   ->getMsRunP()
+                   ->getXmlId());
   _output_stream->writeAttribute("id", xml_id);
   _output_stream->writeAttribute(
     "exp_z",
@@ -739,8 +737,7 @@ ProticdbMl::writeMatchs(IdentificationGroup *p_identification)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
       // sort protein match by subgroup
-      std::sort(protein_match_list.begin(),
-                protein_match_list.end(),
+      std::sort(protein_match_list.begin(), protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getSubGroupNumber() <
                          b->getGrpProteinSp().get()->getSubGroupNumber();
@@ -853,9 +850,8 @@ ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
               .arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
           // proteinHit.setAttribute("score", "");
           _output_stream->writeAttribute(
-            "rank",
-            QString("%1").arg(
-              p_protein_match->getGrpProteinSp().get()->getRank()));
+            "rank", QString("%1").arg(
+                      p_protein_match->getGrpProteinSp().get()->getRank()));
 
           // //cvparam
           writeCvParam("PROTICdbO:0000284",
@@ -876,8 +872,7 @@ ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
           // id: PROTICdbO:0000335
           // name: X!TandemPipeline PAI
           writeCvParam("PROTICdbO:0000335",
-                       Utils::getXmlDouble(p_protein_match->getPAI()),
-                       "PAI");
+                       Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
 
           // [Term]
           // id: PROTICdbO:0000337
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 2d3290c4b4c497dc7e541850e70dba28ca0cceff..470c178e00ecc63ba3328af7113ca2af6e6e51fb 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -253,9 +253,8 @@ Xpip::writeIdentificationDataSourceList(
                                      ident_source_sp.get()->getResourceName());
 
       _output_stream->writeAttribute(
-        "engine",
-        QString("%1").arg(static_cast<std::int8_t>(
-          ident_source_sp.get()->getIdentificationEngine())));
+        "engine", QString("%1").arg(static_cast<std::int8_t>(
+                    ident_source_sp.get()->getIdentificationEngine())));
       _output_stream->writeAttribute(
         "version", ident_source_sp.get()->getIdentificationEngineVersion());
 
@@ -318,9 +317,9 @@ Xpip::writeMsrunList(const MsRunStore &msrun_store)
       _output_stream->writeStartElement("msrun");
       _output_stream->writeAttribute("id", msrun_sp.get()->getXmlId());
       _output_stream->writeAttribute("name", msrun_sp.get()->getSampleName());
-      _output_stream->writeAttribute("format",
-                                     QString("%1").arg(static_cast<std::int8_t>(
-                                       msrun_sp.get()->getMzFormat())));
+      _output_stream->writeAttribute(
+        "format", QString("%1").arg(
+                    static_cast<std::int8_t>(msrun_sp.get()->getMzFormat())));
       QFileInfo mz_info(msrun_sp.get()->getFilename());
       if(mz_info.exists())
         {
@@ -592,9 +591,8 @@ Xpip::writePeptideEvidence(const PeptideEvidence *p_peptide_evidence)
     "scan", QString("%1").arg(p_peptide_evidence->getScan()));
   writeDoubleAttribute("rt", p_peptide_evidence->getRetentionTime());
   _output_stream->writeAttribute(
-    "eng",
-    QString("%1").arg(
-      (unsigned int)p_peptide_evidence->getIdentificationEngine()));
+    "eng", QString("%1").arg(
+             (unsigned int)p_peptide_evidence->getIdentificationEngine()));
   writeDoubleAttribute("evalue", p_peptide_evidence->getEvalue());
   writeDoubleAttribute("exp_mass", p_peptide_evidence->getExperimentalMass());
   _output_stream->writeAttribute(
diff --git a/src/utils/httpversion.cpp b/src/utils/httpversion.cpp
index cd76e5f5967adeca86f23ebbd528dcfcced894f8..582fd54daf7a1b0c6dc126044af2e91cd557da4d 100644
--- a/src/utils/httpversion.cpp
+++ b/src/utils/httpversion.cpp
@@ -48,9 +48,7 @@ HttpVersion::HttpVersion()
     {
       mpa_manager = new QNetworkAccessManager();
       QObject::connect(
-        mpa_manager,
-        &QNetworkAccessManager::finished,
-        this,
+        mpa_manager, &QNetworkAccessManager::finished, this,
         [=](QNetworkReply *reply) {
           if(reply->error())
             {
@@ -77,12 +75,11 @@ HttpVersion::HttpVersion()
 
       m_request.setHeader(QNetworkRequest::ContentTypeHeader,
                           "application/json");
-      m_request.setRawHeader("User-Agent",
-                             QString("%1 %2 (%3)")
-                               .arg(SOFTWARE_NAME)
-                               .arg(XTPCPP_VERSION)
-                               .arg(BUILD_SYSTEM_NAME)
-                               .toLatin1());
+      m_request.setRawHeader("User-Agent", QString("%1 %2 (%3)")
+                                             .arg(SOFTWARE_NAME)
+                                             .arg(XTPCPP_VERSION)
+                                             .arg(BUILD_SYSTEM_NAME)
+                                             .toLatin1());
       mpa_manager->get(m_request);
     }
 }
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index d5312dc8828fbbb6b9d6c5b9da2a73bccb72d0ab..f867fb0b9e92017998c12f762f545393eff8288f 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -46,9 +46,8 @@ MsRunSp
 MsRunStore::getInstance(const MsRun *p_msrun)
 {
   auto it = std::find_if(
-    _map_msrun.begin(), _map_msrun.end(), [p_msrun](const MsRunSp &msrun_sp) {
-      return msrun_sp.get() == p_msrun;
-    });
+    _map_msrun.begin(), _map_msrun.end(),
+    [p_msrun](const MsRunSp &msrun_sp) { return msrun_sp.get() == p_msrun; });
   if(it != _map_msrun.end())
     {
       return (*it);
@@ -66,8 +65,7 @@ MsRunStore::getInstance(const QString &location)
   if(file_ondisk.baseName() == location)
     {
       // look only for the same sample name
-      it = std::find_if(_map_msrun.begin(),
-                        _map_msrun.end(),
+      it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
                         [location](const MsRunSp &msrun_sp) {
                           return msrun_sp.get()->getSampleName() == location;
                         });
@@ -75,8 +73,7 @@ MsRunStore::getInstance(const QString &location)
   else
     {
       // look for an absolute file path
-      it = std::find_if(_map_msrun.begin(),
-                        _map_msrun.end(),
+      it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
                         [location](const MsRunSp &msrun_sp) {
                           if(msrun_sp.get()->getSampleName() ==
                              msrun_sp.get()->getFilename())
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index ea5318fa38497723202d5f04b834b4f2e5c905b7..a99100907b1a2bb2535c079b58b4673194b294d4 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -129,9 +129,7 @@ PeptideEvidenceStore::getPeptideEvidenceList() const
 void
 PeptideEvidenceStore::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
 {
   for(const PeptideEvidenceSp &peptide_evidence_sp : _peptide_evidence_list)
     {
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index ed356fc648ac444e32d87b3439c79ad6b407694f..515cc660572c66a501881799e863a5ca19134e5b 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -70,8 +70,7 @@ class PeptideEvidenceStore
    */
   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: