Code Arrangement Changes #8 (#5476)

Co-authored-by: Arraxx <kumaramanjha2901@gmail.com>
OpenMS · Aug 7, 2021 · e4434b2 · e4434b2
1 parent 962916f
commit e4434b2
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Showing 50 changed files with 926 additions and 525 deletions.
diff --git a/src/openms/source/FORMAT/ConsensusXMLFile.cpp b/src/openms/source/FORMAT/ConsensusXMLFile.cpp
@@ -258,7 +258,9 @@ namespace OpenMS
       String file_version = "";
       optionalAttributeAsString_(file_version, attributes, "version");
       if (file_version == "")
+      {
         file_version = "1.0"; //default version is 1.0
+      }
       if (file_version.toDouble() > version_.toDouble())
       {
         warning(LOAD, "The XML file (" + file_version + ") is newer than the parser (" + version_ + "). This might lead to undefined program behavior.");

diff --git a/src/openms/source/FORMAT/ControlledVocabulary.cpp b/src/openms/source/FORMAT/ControlledVocabulary.cpp
@@ -209,8 +209,9 @@ namespace OpenMS
 
       //do nothing for empty lines
       if (line == "")
+      {
         continue;
-
+      }
       //********************************************************************************
       //stanza line
       if (line_wo_spaces[0] == '[')
@@ -292,7 +293,9 @@ namespace OpenMS
             //check if the parent term name is correct
             String parent_name = line.suffix('!').trim();
             if (!checkName_(parent_id, parent_name))
+            {
               cerr << "Warning: while loading term '" << term.id << "' of CV '" << name_ << "': part_of relationship term name '" << parent_name << "' and id '" << parent_id << "' differ." << "\n";
+            }
           }
           else
           {
@@ -309,7 +312,9 @@ namespace OpenMS
             //check if the parent term name is correct
             String unit_name = line.suffix('!').trim();
             if (!checkName_(unit_id, unit_name))
+            {
               cerr << "Warning: while loading term '" << term.id << "' of CV '" << name_ << "': has_units relationship term name '" << unit_name << "' and id '" << unit_id << "' differ." << "\n";
+            }
           }
           else
           {
@@ -572,8 +577,9 @@ namespace OpenMS
   bool ControlledVocabulary::checkName_(const String& id, const String& name, bool ignore_case)
   {
     if (!exists(id))
+    {
       return true; //what?!
-
+    }
     String parent_name = name;
     String real_parent_name = getTerm(id).name;
 

diff --git a/src/openms/source/FORMAT/DATAACCESS/MSDataSqlConsumer.cpp b/src/openms/source/FORMAT/DATAACCESS/MSDataSqlConsumer.cpp
@@ -84,18 +84,28 @@ namespace OpenMS
   {
     spectra_.push_back(s);
     s.clear(false);
-    if (full_meta_) peak_meta_.addSpectrum(s);
-
-    if (spectra_.size() >= flush_after_) {flush();}
+    if (full_meta_)
+    {
+      peak_meta_.addSpectrum(s);
+    }
+    if (spectra_.size() >= flush_after_)
+    {
+      flush();
+    }
   }
 
   void MSDataSqlConsumer::consumeChromatogram(ChromatogramType & c)
   {
     chromatograms_.push_back(c);
     c.clear(false);
-    if (full_meta_) peak_meta_.addChromatogram(c);
-
-    if (chromatograms_.size() >= flush_after_) {flush();}
+    if (full_meta_)
+    {
+      peak_meta_.addChromatogram(c);
+    }
+    if (chromatograms_.size() >= flush_after_)
+    {
+      flush();
+    }
   }
 
   void MSDataSqlConsumer::setExpectedSize(Size /* expectedSpectra */, Size /* expectedChromatograms */) {;}

diff --git a/src/openms/source/FORMAT/DATAACCESS/MSDataTransformingConsumer.cpp b/src/openms/source/FORMAT/DATAACCESS/MSDataTransformingConsumer.cpp
@@ -85,6 +85,9 @@ namespace OpenMS
       void MSDataTransformingConsumer::setExperimentalSettings(const OpenMS::ExperimentalSettings& es)
       { 
         // apply the given function to it (unless nullptr)
-        if (lambda_exp_settings_) lambda_exp_settings_(es);        
+        if (lambda_exp_settings_)
+        {
+          lambda_exp_settings_(es);
+        }        
       }
 } // namespace OpenMS
diff --git a/src/openms/source/FORMAT/DATAACCESS/MSDataWritingConsumer.cpp b/src/openms/source/FORMAT/DATAACCESS/MSDataWritingConsumer.cpp
@@ -187,8 +187,9 @@ namespace OpenMS
 
     // Only write the footer if we actually did start writing ... 
     if (started_writing_) 
+    {
       Internal::MzMLHandlerHelper::writeFooter_(ofs_, options_, spectra_offsets_, chromatograms_offsets_);
-
+    }
     delete validator_;
     ofs_.close();
   }

diff --git a/src/openms/source/FORMAT/DATAACCESS/SiriusFragmentAnnotation.cpp b/src/openms/source/FORMAT/DATAACCESS/SiriusFragmentAnnotation.cpp
@@ -133,13 +133,13 @@ namespace OpenMS
       {
         if (line.hasPrefix(n_id_prefix))
         {
-           String n_id = line.erase(line.find(n_id_prefix), n_id_prefix.size());
-           ext_n_ids.emplace_back(n_id);
+          String n_id = line.erase(line.find(n_id_prefix), n_id_prefix.size());
+          ext_n_ids.emplace_back(n_id);
         }
         else if (spectrum_ms_file.eof())
         {
-           OPENMS_LOG_WARN << "No native id was found - please check your input mzML. " << std::endl;
-           break;
+          OPENMS_LOG_WARN << "No native id was found - please check your input mzML. " << std::endl;
+          break;
         }
       }
       spectrum_ms_file.close();

diff --git a/src/openms/source/FORMAT/FeatureXMLFile.cpp b/src/openms/source/FORMAT/FeatureXMLFile.cpp
@@ -400,7 +400,9 @@ namespace OpenMS
     else if (tag == "featureList")
     {
       if (options_.getMetadataOnly())
+      {
         throw EndParsingSoftly(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
+      }
       Size count = attributeAsInt_(attributes, "count");
       if (size_only_) // true if loadSize() was used instead of load()
       {
@@ -812,8 +814,9 @@ namespace OpenMS
     }
 
     if (disable_parsing_)
+    {
       return;
-
+    }
     // do the actual parsing:
     open_tags_.pop_back();
 
@@ -823,8 +826,9 @@ namespace OpenMS
       in_description_ = false;
     }
     if (in_description_)
+    {
       return;
-
+    }
     if (tag == "feature")
     {
       if ((!options_.hasRTRange() || options_.getRTRange().encloses(current_feature_->getRT()))
@@ -933,18 +937,21 @@ namespace OpenMS
   {
     // handle skipping of whole sections
     if (disable_parsing_)
+    {
       return;
-
+    }
     // do the actual parsing:
 
     //for downward compatibility, all tags in the old description must be ignored
     if (in_description_)
+    {
       return;
-
+    }
     // we are before first tag or beyond last tag
     if (open_tags_.size() == 0)
+    {
       return;
-
+    }
     String& current_tag = open_tags_.back();
     if (current_tag == "intensity")
     {

diff --git a/src/openms/source/FORMAT/FileHandler.cpp b/src/openms/source/FORMAT/FileHandler.cpp
@@ -456,7 +456,9 @@ namespace OpenMS
         conversion_error = true;
       }
       if (!conversion_error)
+      {
         return FileTypes::DTA;
+      }
     }
 
     //DTA2D
@@ -475,7 +477,9 @@ namespace OpenMS
         conversion_error = true;
       }
       if (!conversion_error)
+      {
         return FileTypes::DTA2D;
+      }
     }
 
     // MGF (Mascot Generic Format)

diff --git a/src/openms/source/FORMAT/FileTypes.cpp b/src/openms/source/FORMAT/FileTypes.cpp
@@ -131,7 +131,10 @@ namespace OpenMS
   {
     for (const auto& t : type_list_)
     {
-      if (t == type) return true;
+      if (t == type)
+      {
+        return true;
+      }
     }
     return false;
   }
@@ -161,8 +164,10 @@ namespace OpenMS
       }
       out += ListUtils::concatenate(items, "");
     }
-    if (add_all_filter) out += "all files (*);;";
-
+    if (add_all_filter)
+    {
+      out += "all files (*);;";
+    }
     // remove the last ";;", since this will be interpreted as ' (*)' by Qt
     out = out.chop(2);
 
@@ -174,7 +179,10 @@ namespace OpenMS
   {
     for (const auto& t_info : type_with_annotation__)
     {
-      if (t_info.type == type) return t_info.name;
+      if (t_info.type == type)
+      {
+        return t_info.name;
+      }
     }
     throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Type has no name!", String(type));
   }
@@ -195,7 +203,10 @@ namespace OpenMS
 
     for (const auto& t_info : type_with_annotation__)
     {
-      if (String(t_info.name).toUpper() == name_upper) return t_info.type;
+      if (String(t_info.name).toUpper() == name_upper)
+      {
+        return t_info.type;
+      }
     }
 
     return FileTypes::UNKNOWN;