Code Arrangement Changes #7 (#5471)

* Code Arrangement Changes #7 * Update ClusterAnalyzer.cpp Co-authored-by: Arraxx <kumaramanjha2901@gmail.com>
OpenMS · Aug 3, 2021 · b47dbde · b47dbde
1 parent c2555c3
commit b47dbde
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Showing 26 changed files with 265 additions and 145 deletions.
diff --git a/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp b/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp
@@ -41,12 +41,9 @@
 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.h>
 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.h>
 
-namespace OpenMS
+namespace OpenMS::ims
 {
 
-  namespace ims
-  {
-
     const IMSAlphabet::name_type & IMSAlphabet::getName(size_type index) const
     {
       return getElement(index).getName();
@@ -174,5 +171,4 @@ namespace OpenMS
       return os;
     }
 
-  } // namespace ims
-} // namespace OpenMS
+} // namespace OpenMS // namespace ims
diff --git a/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp b/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp
@@ -81,7 +81,10 @@ namespace OpenMS
   {
     OPENMS_PRECONDITION(ps.isSorted(), "Spectrum needs to be sorted by m/z.");
 
-    if (ps.empty()) { return; }
+    if (ps.empty())
+    { 
+      return;
+    }
 
     bins_ = EmptySparseVector;
 
@@ -120,15 +123,20 @@ namespace OpenMS
     }
 
     // efficient look-up of number of non-zero entries, so we use this as-well
-    if (bins_.nonZeros() != rhs.bins_.nonZeros()) { return false; }
+    if (bins_.nonZeros() != rhs.bins_.nonZeros())
+    {
+      return false;
+    }
 
     // test non-sparse (non-zero) elements for equality
     SparseVectorIteratorType it(bins_);
     SparseVectorIteratorType rhs_it(rhs.bins_);  
     while (it)      
     {
-      if (it.index() != rhs_it.index()
-       || it.value() != rhs_it.value()) { return false; }
+      if (it.index() != rhs_it.index() || it.value() != rhs_it.value())
+      {
+        return false;
+      }
       ++it;
       ++rhs_it;
     }

diff --git a/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp b/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
@@ -85,10 +85,14 @@ namespace OpenMS
     // shortcut similarity calculation by comparing PrecursorPeaks (PrecursorPeaks more than delta away from each other are supposed to be from another peptide)
     double pre_mz1 = 0.0;
     if (!spec1.getPrecursors().empty())
+    {
       pre_mz1 = spec1.getPrecursors()[0].getMZ();
+    }
     double pre_mz2 = 0.0;
     if (!spec2.getPrecursors().empty())
+    {
       pre_mz2 = spec2.getPrecursors()[0].getMZ();
+    }
     if (fabs(pre_mz1 - pre_mz2) > (double)param_.getValue("precursor_mass_tolerance"))
     {
       return 0;

diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp
@@ -97,11 +97,16 @@ namespace OpenMS
 
     // calculate sum of squared intensities
     double sum1(0);
-    for (auto const & p : s1) { sum1 += pow(p.getIntensity(), 2); }
+    for (auto const & p : s1)
+    { 
+      sum1 += pow(p.getIntensity(), 2);
+    }
 
     double sum2(0);
-    for (auto const & p : s2) { sum2 += pow(p.getIntensity(), 2); }
-
+    for (auto const & p : s2)
+    { 
+      sum2 += pow(p.getIntensity(), 2);
+    }
     for (auto const & ap : alignment)
     {
       const double mz_tolerance = is_relative_tolerance ? tolerance * s1[ap.first].getMZ() * 1e-6 : tolerance;

diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp
@@ -111,9 +111,13 @@ namespace OpenMS
     lastconsensus_ = PeakSpectrum();
     Precursor p1, p2;
     if (!x.getPrecursors().empty())
+    {
       p1 = x.getPrecursors()[0];
+    }
     if (!y.getPrecursors().empty())
+    {
       p2 = y.getPrecursors()[0];
+    }
     lastconsensus_.getPrecursors().resize(1);
     lastconsensus_.getPrecursors()[0].setMZ((p1.getMZ() + p2.getMZ()) / 2);
     lastconsensus_.getPrecursors()[0].setCharge(p1.getCharge());
@@ -174,9 +178,13 @@ namespace OpenMS
             yrun++;
           }
           if (xit + xrun == x.end())
+          {
             break;
+          }
           if (yit + yrun == y.end())
+          {
             break;
+          }
         }
 
         //dynamic programming necessary to calculate optimal pairing
@@ -292,7 +300,9 @@ namespace OpenMS
         consensuspeak.setMZ(x[xstart + i - 1].getMZ());
         consensuspeak.setIntensity((x[xstart + i - 1].getIntensity()) * (1 - factor_));
         if (keeppeaks_)
+        {
           lastconsensus_.push_back(consensuspeak);
+        }
         i--;
       }
       else if (trace[i][j] == -1)
@@ -301,11 +311,15 @@ namespace OpenMS
         consensuspeak.setMZ(y[ystart + j - 1].getMZ());
         consensuspeak.setIntensity((y[ystart + j - 1].getIntensity()) * factor_);
         if (keeppeaks_)
+        {
           lastconsensus_.push_back(consensuspeak);
+        }
         j--;
       }
       if (!i || !j)
+      {
         break;
+      }
     }
 
     return dparray[xend - xstart + 1][yend - ystart + 1];

diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp
@@ -78,10 +78,14 @@ namespace OpenMS
 
     double mz1 = 0.0;
     if (!x.getPrecursors().empty())
+    {
       mz1 = x.getPrecursors()[0].getMZ();
+    }
     double mz2 = 0.0;
     if (!y.getPrecursors().empty())
+    {
       mz2 = y.getPrecursors()[0].getMZ();
+    }
 
     if (fabs(mz1 - mz2) > window)
     {

diff --git a/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp b/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp
@@ -103,16 +103,16 @@ namespace OpenMS
     std::cout << std::endl;
     std::cout << s2 << std::endl;*/
 
-    for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
+    for (const Peak1D& it1 : s1)
     {
-      double temp = it1->getIntensity();
+      double temp = it1.getIntensity();
       sum1 += temp * temp;
       sum3 += temp;
     }
 
-    for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
+    for (const Peak1D& it1 : s2)
     {
-      double temp = it1->getIntensity();
+      double temp = it1.getIntensity();
       sum2 += temp * temp;
       sum4 += temp;
     }

diff --git a/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp b/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp
@@ -93,9 +93,9 @@ namespace OpenMS
       throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
     }
 
-    for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
+    for (const Peak1D& it1 : s1)
     {
-      sum1 += it1->getIntensity();
+      sum1 += it1.getIntensity();
       /*
 for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
 {
@@ -158,9 +158,9 @@ for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
       }
     }*/
 
-    for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
+    for (const Peak1D& it1 : s2)
     {
-      sum2 += it1->getIntensity();
+      sum2 += it1.getIntensity();
       /*
 for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
 {

diff --git a/src/openms/source/CONCEPT/ClassTest.cpp b/src/openms/source/CONCEPT/ClassTest.cpp
@@ -55,12 +55,9 @@
 
 #include <QFileInfo>
 
-namespace OpenMS
+namespace OpenMS::Internal::ClassTest
 {
-  namespace Internal
-  {
-    namespace ClassTest
-    {
+
       bool all_tests = true;
       bool equal_files;
       bool newline = false;
@@ -91,10 +88,6 @@ namespace OpenMS
       std::vector<std::string> tmp_file_list;
       std::vector<UInt> failed_lines_list;
       StringList whitelist;
-    }
-
-    namespace ClassTest
-    {
 
       void mainInit(const char* version, const char* class_name, int argc, const char* argv0)
       {
@@ -443,8 +436,7 @@ namespace OpenMS
         }
       }
 
-      bool
-      isRealSimilar(long double number_1, long double number_2)
+      bool isRealSimilar(long double number_1, long double number_2)
       {
         // Note: The original version of the stuff below was copied from
         // FuzzyStringComparator and then heavily modified for ClassTest.
@@ -571,8 +563,7 @@ namespace OpenMS
         }
       }
 
-      void
-      testStringEqual(const char* /*file*/, int line,
+      void testStringEqual(const char* /*file*/, int line,
                       const std::string& string_1,
                       const char* string_1_stringified,
                       const std::string& string_2,
@@ -684,7 +675,4 @@ namespace OpenMS
 
         return result;
       }
-
-    }
-  }
 }
diff --git a/src/openms/source/CONCEPT/FuzzyStringComparator.cpp b/src/openms/source/CONCEPT/FuzzyStringComparator.cpp
@@ -300,8 +300,10 @@ namespace OpenMS
   bool FuzzyStringComparator::compareLines_(std::string const& line_str_1, std::string const& line_str_2)
   {
     // in most cases, results will be identical. If not, do the expensive fuzzy compare
-    if (line_str_1 == line_str_2) return true;
-
+    if (line_str_1 == line_str_2)
+    {
+      return true;
+    }
     for (StringList::const_iterator slit = whitelist_.begin();
          slit != whitelist_.end(); ++slit)
     {
@@ -350,8 +352,10 @@ namespace OpenMS
 #ifdef DEBUG_FUZZY
             std::cout << "cmp number: " << String(element_1_.number) << " : " << String(element_2_.number) << std::endl;
 #endif
-            if (element_1_.number == element_2_.number) continue;
-
+            if (element_1_.number == element_2_.number)
+            {
+              continue;
+            }
             // check if absolute difference is small
             double absdiff = element_1_.number - element_2_.number;
             if (absdiff < 0)
@@ -666,7 +670,9 @@ namespace OpenMS
            wlcit != whitelist_cases_.end(); ++wlcit)
       {
         if (wlcit->first.size() > length)
+        {
           length = wlcit->first.size();
+        }
       }
       for (std::map<String, UInt>::const_iterator wlcit = whitelist_cases_.begin();
            wlcit != whitelist_cases_.end(); ++wlcit)

diff --git a/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp b/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp
@@ -53,12 +53,9 @@
 
 #define OPENMS_CORE_DUMP_ENVNAME "OPENMS_DUMP_CORE"
 
-namespace OpenMS
+namespace OpenMS::Exception
 {
 
-  namespace Exception
-  {
-
     GlobalExceptionHandler::GlobalExceptionHandler() throw()
     {
       std::set_terminate(terminate);
@@ -143,6 +140,5 @@ namespace OpenMS
       GlobalExceptionHandler::line_() = line;
     }
 
-  } // namespace Exception
 
-} // namespace OpenMS
+} // namespace OpenMS // namespace Exception
diff --git a/src/openms/source/CONCEPT/Init.cpp b/src/openms/source/CONCEPT/Init.cpp
@@ -36,28 +36,25 @@
 
 #include <xercesc/util/PlatformUtils.hpp>
 
-namespace OpenMS
+namespace OpenMS::Internal
 {
-  namespace Internal
-  {
 
-    // Initialize xerces
-    // see ticket #352 for more details
-    struct xerces_init
+  // Initialize xerces
+  // see ticket #352 for more details
+  struct xerces_init
+  {
+    xerces_init() 
     {
-      xerces_init() 
-      {
-        xercesc::XMLPlatformUtils::Initialize();
-      }
+      xercesc::XMLPlatformUtils::Initialize();
+    }
 
-      ~xerces_init() 
-      {
-        xercesc::XMLPlatformUtils::Terminate();
-      }
+    ~xerces_init() 
+    {
+      xercesc::XMLPlatformUtils::Terminate();
+    }
 
-    };
-    const xerces_init xinit;
+  };
+  const xerces_init xinit;
 
-  }
-}
+} //OpenMS //Internal