Code Arrangement changes #2 (OpenMS#5406)

Co-authored-by: Arraxx <[email protected]>
Roestlab · Jul 11, 2021 · a146aed · a146aed
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commit a146aed
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Showing 4 changed files with 34 additions and 26 deletions.
diff --git a/src/openms/source/ANALYSIS/ID/ConsensusIDAlgorithm.cpp b/src/openms/source/ANALYSIS/ID/ConsensusIDAlgorithm.cpp
@@ -90,14 +90,13 @@ namespace OpenMS
     number_of_runs_ = (number_of_runs != 0) ? number_of_runs : ids.size();
 
     // prepare data here, so that it doesn't have to happen in each algorithm:
-    for (vector<PeptideIdentification>::iterator pep_it = ids.begin(); 
-         pep_it != ids.end(); ++pep_it)
+    for (PeptideIdentification& pep : ids)
     {
-      pep_it->sort();
+      pep.sort();
       if ((considered_hits_ > 0) &&
-          (pep_it->getHits().size() > considered_hits_))
+          (pep.getHits().size() > considered_hits_))
       {
-        pep_it->getHits().resize(considered_hits_);
+        pep.getHits().resize(considered_hits_);
       }
     }
     // make sure there are no duplicated hits (by sequence):

diff --git a/src/openms/source/CHEMISTRY/AASequence.cpp b/src/openms/source/CHEMISTRY/AASequence.cpp
@@ -234,8 +234,10 @@ namespace OpenMS
     const AASequence& seq = *this;
 
     String bs;
-    if (seq.empty()) return bs;
-
+    if (seq.empty())
+    {
+      return bs;
+    }
     if (seq.hasNTerminalModification())
     {
       const ResidueModification& mod = *(seq.getNTerminalModification());
@@ -245,8 +247,10 @@ namespace OpenMS
       if (std::find(fixed_modifications.begin(), fixed_modifications.end(), nterm_mod_name) == fixed_modifications.end())
       {
         double nominal_mass = mod.getDiffMonoMass();
-        if (!mass_delta) nominal_mass += Residue::getInternalToNTerm().getMonoWeight();
-
+       if (!mass_delta)
+        {
+          nominal_mass += Residue::getInternalToNTerm().getMonoWeight();
+        }
         String sign = (mass_delta && nominal_mass > 0) ? "+" : ""; // the '-' will be printed automatically by conversion to string
         if (integer_mass)
         {
@@ -271,9 +275,14 @@ namespace OpenMS
         if (std::find(fixed_modifications.begin(), fixed_modifications.end(), mod_name) == fixed_modifications.end())
         {
           double nominal_mass;
-          if (mass_delta) nominal_mass = mod.getDiffMonoMass();
-          else nominal_mass = r.getMonoWeight(Residue::Internal);
-
+          if (mass_delta)
+          {
+            nominal_mass = mod.getDiffMonoMass();
+          }
+          else 
+          {
+            nominal_mass = r.getMonoWeight(Residue::Internal);
+          }
           String sign = (mass_delta && nominal_mass > 0) ? "+" : "";
           if (aa == "X")
           {

diff --git a/src/openms/source/FILTERING/ID/IDFilter.cpp b/src/openms/source/FILTERING/ID/IDFilter.cpp
@@ -478,8 +478,10 @@ namespace OpenMS
       const vector<ProteinIdentification::ProteinGroup>& groups,
       vector<ProteinHit>& hits)
   {
-    if (hits.empty()) return; // nothing to update
-
+    if (hits.empty())
+    {
+      return; // nothing to update
+    }
     // we'll do lots of look-ups, so use a suitable data structure:
     unordered_set<String> valid_accessions;
     for (const auto& grp : groups)
@@ -496,15 +498,14 @@ namespace OpenMS
   void IDFilter::keepBestPeptideHits(vector<PeptideIdentification>& peptides,
                                      bool strict)
   {
-    for (vector<PeptideIdentification>::iterator pep_it = peptides.begin();
-         pep_it != peptides.end(); ++pep_it)
+    for (PeptideIdentification& pep : peptides)
     {
-      vector<PeptideHit>& hits = pep_it->getHits();
+      vector<PeptideHit>& hits = pep.getHits();
       if (hits.size() > 1)
       {
-        pep_it->sort();
+        pep.sort();
         double top_score = hits[0].getScore();
-        bool higher_better = pep_it->isHigherScoreBetter();
+        bool higher_better = pep.isHigherScoreBetter();
         struct HasGoodScore<PeptideHit> good_score(top_score, higher_better);
         if (strict) // only one best score allowed
         {

diff --git a/src/openms/source/TRANSFORMATIONS/FEATUREFINDER/SeedListGenerator.cpp b/src/openms/source/TRANSFORMATIONS/FEATUREFINDER/SeedListGenerator.cpp
@@ -65,22 +65,21 @@ namespace OpenMS
                                            bool use_peptide_mass)
   {
     seeds.clear();
-    for (vector<PeptideIdentification>::iterator pep_it = peptides.begin();
-         pep_it != peptides.end(); ++pep_it)
+    for (PeptideIdentification& pep : peptides)
     {
       double mz;
-      if (!pep_it->getHits().empty() && use_peptide_mass)
+      if (!pep.getHits().empty() && use_peptide_mass)
       {
-        pep_it->sort();
-        const PeptideHit& hit = pep_it->getHits().front();
+        pep.sort();
+        const PeptideHit& hit = pep.getHits().front();
         Int charge = hit.getCharge();
         mz = hit.getSequence().getMZ(charge);
       }
       else
       {
-        mz = pep_it->getMZ();
+        mz = pep.getMZ();
       }
-      DPosition<2> point(pep_it->getRT(), mz);
+      DPosition<2> point(pep.getRT(), mz);
       seeds.push_back(point);
     }
   }