Changes in / [7dc102:cb2146]

Location:

src

Files:

• Descriptors/MoleculeIdDescriptor.cpp (added)
• Descriptors/MoleculeIdDescriptor.hpp (added)
• Descriptors/MoleculeIdDescriptor_impl.hpp (added)
• Makefile.am (modified) (1 diff)
• Parser/TremoloParser.hpp (modified) (1 diff)
• World.cpp (modified) (2 diffs)
• World.hpp (modified) (2 diffs)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• unittests/AtomDescriptorTest.cpp (added)
• unittests/AtomDescriptorTest.hpp (added)
• unittests/DescriptorUnittest.cpp (deleted)
• unittests/DescriptorUnittest.hpp (deleted)
• unittests/Makefile.am (modified) (7 diffs)
• unittests/MoleculeDescriptorTest.cpp (added)
• unittests/MoleculeDescriptorTest.hpp (added)
• unittests/atomsCalculationTest.cpp (modified) (3 diffs)
• unittests/manipulateAtomsTest.cpp (modified) (2 diffs)

src/Makefile.am

@@ -32 +32 @@
 LEGACYHEADER = Legacy/oldmenu.hpp
 
-DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp Descriptors/AtomTypeDescriptor.cpp Descriptors/MoleculeDescriptor.cpp
-DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp Descriptors/MoleculeDescriptor.hpp
+DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
+                                   Descriptors/AtomIdDescriptor.cpp \
+                                   Descriptors/AtomTypeDescriptor.cpp \
+                                   Descriptors/MoleculeDescriptor.cpp \
+                                   Descriptors/MoleculeIdDescriptor.cpp
+                                   
+DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp \
+                                   Descriptors/AtomIdDescriptor.hpp \
+                                   Descriptors/AtomTypeDescriptor.hpp \
+                                   Descriptors/MoleculeDescriptor.hpp \
+                                   Descriptors/MoleculeIdDescriptor.hpp
 
 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PARSERSOURCE} ${PATTERNSOURCE} ${UISOURCE} ${DESCRIPTORSOURCE} ${LEGACYSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp lists.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp World.cpp WorldIterators.cpp

src/Parser/TremoloParser.hpp

@@ -18 +18 @@
 
 private:
-  map<string, string> moreData;
+  map<std::string, std::string> moreData;
 };
 

src/World.cpp

@@ -159 +159 @@
 /******************************* IDManagement *****************************/
 
+// Atoms
+
 atomId_t World::getNextAtomId(){
   // see if we can reuse some Id
@@ -199 +201 @@
   }
 }
+
+// Molecules
+
 /******************************* Iterators ********************************/
 

src/World.hpp

@@ -151 +151 @@
   // Atoms
 
-  class AtomIterator {
+  class AtomIterator :
+    public std::iterator<std::iterator_traits<AtomSet::iterator>::difference_type,
+                         std::iterator_traits<AtomSet::iterator>::value_type,
+                         std::iterator_traits<AtomSet::iterator>::pointer,
+                         std::iterator_traits<AtomSet::iterator>::reference>
+  {
   public:
+
+    typedef AtomSet::iterator _Iter;
+    typedef _Iter::value_type value_type;
+    typedef _Iter::difference_type difference_type;
+    typedef _Iter::pointer pointer;
+    typedef _Iter::reference reference;
+    typedef _Iter::iterator_category iterator_category;
+
+
     AtomIterator();
     AtomIterator(AtomDescriptor, World*);
@@ -191 +205 @@
   // Molecules
 
-  class MoleculeIterator {
+  class MoleculeIterator :
+    public std::iterator<std::iterator_traits<MoleculeSet::iterator>::difference_type,
+                         std::iterator_traits<MoleculeSet::iterator>::value_type,
+                         std::iterator_traits<MoleculeSet::iterator>::pointer,
+                         std::iterator_traits<MoleculeSet::iterator>::reference>
+  {
   public:
+
+    typedef MoleculeSet::iterator _Iter;
+    typedef _Iter::value_type value_type;
+    typedef _Iter::difference_type difference_type;
+    typedef _Iter::pointer pointer;
+    typedef _Iter::reference reference;
+    typedef _Iter::iterator_category iterator_category;
+
     MoleculeIterator();
     MoleculeIterator(MoleculeDescriptor, World*);

src/atom.cpp

@@ -306 +306 @@
 }
 
-int atom::getId() {
+atomId_t atom::getId() {
   return id;
 }

src/atom.hpp

@@ -79 +79 @@
   void setWorld(World*);
 
-  virtual int getId();
+  virtual atomId_t getId();
   virtual bool changeId(atomId_t newId);
 

src/unittests/Makefile.am

@@ -12 +12 @@
   AnalysisCorrelationToSurfaceUnitTest \
   AnalysisPairCorrelationUnitTest \
+  atomsCalculationTest \
+  AtomDescriptorTest \
   BondGraphUnitTest \
+  CacheableTest \
   GSLMatrixSymmetricUnitTest \
   GSLMatrixUnitTest \
@@ -20 +23 @@
   ListOfBondsUnitTest \
   LogUnitTest \
+  manipulateAtomsTest \
   MemoryUsageObserverUnitTest \
   MemoryAllocatorUnitTest \
+  MoleculeDescriptorTest \
+  ObserverTest \
+  ParserUnitTest \
   StackClassUnitTest \
   TesselationUnitTest \
@@ -27 +34 @@
   Tesselation_InOutsideUnitTest \
   VectorUnitTest \
-  ObserverTest \
-  CacheableTest \
-  DescriptorUnittest \
-  ParserUnitTest \
-  manipulateAtomsTest \
-  atomsCalculationTest \
-  ${MENUTESTS}  
-    
+  ${MENUTESTS}
+  
+
   
 check_PROGRAMS = $(TESTS) 
@@ -44 +46 @@
 TESTSOURCES = \
   ActOnAllUnitTest.cpp \
+  ActionSequenceTest.cpp \
   analysisbondsunittest.cpp \
   AnalysisCorrelationToPointUnitTest.cpp \
   AnalysisCorrelationToSurfaceUnitTest.cpp  \
   AnalysisPairCorrelationUnitTest.cpp \
+  AtomDescriptorTest.cpp \
+  atomsCalculationTest.cpp \
   bondgraphunittest.cpp \
+  CacheableTest.cpp \
+  DescriptorUnittest.cpp \
   gslmatrixsymmetricunittest.cpp \
   gslmatrixunittest.cpp \
@@ -56 +63 @@
   listofbondsunittest.cpp \
   logunittest.cpp \
+  manipulateAtomsTest.cpp \
   memoryallocatorunittest.cpp  \
   memoryusageobserverunittest.cpp \
+  MoleculeDescriptorTest.cpp \
+  ObserverTest.cpp \
+  ParserUnitTest.cpp \
   stackclassunittest.cpp \
   tesselationunittest.cpp \
   tesselation_boundarytriangleunittest.cpp \
   tesselation_insideoutsideunittest.cpp \
-  vectorunittest.cpp \
-  ObserverTest.cpp \
-  CacheableTest.cpp \
-  DescriptorUnittest.cpp \
-  ParserUnitTest.cpp \
-  manipulateAtomsTest.cpp \
-  atomsCalculationTest.cpp \
-  ActionSequenceTest.cpp
+  vectorunittest.cpp
 
 TESTHEADERS = \
@@ -119 +123 @@
 MemoryUsageObserverUnitTest_LDADD = ${ALLLIBS}
 
+MoleculeDescriptorTest_SOURCES = UnitTestMain.cpp MoleculeDescriptorTest.cpp MoleculeDescriptorTest.hpp
+MoleculeDescriptorTest_LDADD = ${ALLLIBS}
+
 StackClassUnitTest_SOURCES = UnitTestMain.cpp stackclassunittest.cpp stackclassunittest.hpp
 StackClassUnitTest_LDADD = ${ALLLIBS}
@@ -143 +150 @@
 CacheableTest_LDADD = ${ALLLIBS}
 
-DescriptorUnittest_SOURCES = UnitTestMain.cpp DescriptorUnittest.cpp DescriptorUnittest.hpp
-DescriptorUnittest_LDADD = ${ALLLIBS}
+AtomDescriptorTest_SOURCES = UnitTestMain.cpp AtomDescriptorTest.cpp AtomDescriptorTest.hpp
+AtomDescriptorTest_LDADD = ${ALLLIBS}
 
 ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp

src/unittests/atomsCalculationTest.cpp

@@ -30 +30 @@
 class AtomStub : public atom {
 public:
-  AtomStub(int _id) :
+  AtomStub(atomId_t _id) :
   atom(),
   id(_id),
@@ -36 +36 @@
   {}
 
-  virtual int getId(){
+  virtual atomId_t getId(){
     return id;
   }
@@ -46 +46 @@
   bool manipulated;
 private:
-  int id;
+  atomId_t id;
 };
 

src/unittests/manipulateAtomsTest.cpp

@@ -34 +34 @@
   {}
 
-  virtual int getId(){
+  virtual atomId_t getId(){
     return id;
   }
@@ -44 +44 @@
   bool manipulated;
 private:
-  int id;
+  atomId_t id;
 };