Changes in / [cb2146:7dc102]


Ignore:
Location:
src
Files:
2 added
7 deleted
9 edited

Legend:

Unmodified
Added
Removed

  • src/Makefile.am

    rcb2146 r7dc102  
    3232LEGACYHEADER = Legacy/oldmenu.hpp
    3333
    34 DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    35                                    Descriptors/AtomIdDescriptor.cpp \
    36                                    Descriptors/AtomTypeDescriptor.cpp \
    37                                    Descriptors/MoleculeDescriptor.cpp \
    38                                    Descriptors/MoleculeIdDescriptor.cpp
    39                                    
    40 DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp \
    41                                    Descriptors/AtomIdDescriptor.hpp \
    42                                    Descriptors/AtomTypeDescriptor.hpp \
    43                                    Descriptors/MoleculeDescriptor.hpp \
    44                                    Descriptors/MoleculeIdDescriptor.hpp
     34DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp Descriptors/AtomTypeDescriptor.cpp Descriptors/MoleculeDescriptor.cpp
     35DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp Descriptors/MoleculeDescriptor.hpp
    4536
    4637SOURCE = ${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

    rcb2146 r7dc102  
    1818
    1919private:
    20   map<std::string, std::string> moreData;
     20  map<string, string> moreData;
    2121};
    2222

  • src/World.cpp

    rcb2146 r7dc102  
    159159/******************************* IDManagement *****************************/
    160160
    161 // Atoms
    162 
    163161atomId_t World::getNextAtomId(){
    164162  // see if we can reuse some Id
    … …  
    201199  }
    202200}
    203 
    204 // Molecules
    205 
    206201/******************************* Iterators ********************************/
    207202

  • src/World.hpp

    rcb2146 r7dc102  
    151151  // Atoms
    152152
    153   class AtomIterator :
    154     public std::iterator<std::iterator_traits<AtomSet::iterator>::difference_type,
    155                          std::iterator_traits<AtomSet::iterator>::value_type,
    156                          std::iterator_traits<AtomSet::iterator>::pointer,
    157                          std::iterator_traits<AtomSet::iterator>::reference>
    158   {
     153  class AtomIterator {
    159154  public:
    160 
    161     typedef AtomSet::iterator _Iter;
    162     typedef _Iter::value_type value_type;
    163     typedef _Iter::difference_type difference_type;
    164     typedef _Iter::pointer pointer;
    165     typedef _Iter::reference reference;
    166     typedef _Iter::iterator_category iterator_category;
    167 
    168 
    169155    AtomIterator();
    170156    AtomIterator(AtomDescriptor, World*);
    … …  
    205191  // Molecules
    206192
    207   class MoleculeIterator :
    208     public std::iterator<std::iterator_traits<MoleculeSet::iterator>::difference_type,
    209                          std::iterator_traits<MoleculeSet::iterator>::value_type,
    210                          std::iterator_traits<MoleculeSet::iterator>::pointer,
    211                          std::iterator_traits<MoleculeSet::iterator>::reference>
    212   {
     193  class MoleculeIterator {
    213194  public:
    214 
    215     typedef MoleculeSet::iterator _Iter;
    216     typedef _Iter::value_type value_type;
    217     typedef _Iter::difference_type difference_type;
    218     typedef _Iter::pointer pointer;
    219     typedef _Iter::reference reference;
    220     typedef _Iter::iterator_category iterator_category;
    221 
    222195    MoleculeIterator();
    223196    MoleculeIterator(MoleculeDescriptor, World*);

  • src/atom.cpp

    rcb2146 r7dc102  
    306306}
    307307
    308 atomId_t atom::getId() {
     308int atom::getId() {
    309309  return id;
    310310}

  • src/atom.hpp

    rcb2146 r7dc102  
    7979  void setWorld(World*);
    8080
    81   virtual atomId_t getId();
     81  virtual int getId();
    8282  virtual bool changeId(atomId_t newId);
    8383

  • src/unittests/Makefile.am

    rcb2146 r7dc102  
    1212  AnalysisCorrelationToSurfaceUnitTest \
    1313  AnalysisPairCorrelationUnitTest \
    14   atomsCalculationTest \
    15   AtomDescriptorTest \
    1614  BondGraphUnitTest \
    17   CacheableTest \
    1815  GSLMatrixSymmetricUnitTest \
    1916  GSLMatrixUnitTest \
    … …  
    2320  ListOfBondsUnitTest \
    2421  LogUnitTest \
    25   manipulateAtomsTest \
    2622  MemoryUsageObserverUnitTest \
    2723  MemoryAllocatorUnitTest \
    28   MoleculeDescriptorTest \
    29   ObserverTest \
    30   ParserUnitTest \
    3124  StackClassUnitTest \
    3225  TesselationUnitTest \
    … …  
    3427  Tesselation_InOutsideUnitTest \
    3528  VectorUnitTest \
    36   ${MENUTESTS}
    37  
    38 
     29  ObserverTest \
     30  CacheableTest \
     31  DescriptorUnittest \
     32  ParserUnitTest \
     33  manipulateAtomsTest \
     34  atomsCalculationTest \
     35  ${MENUTESTS} 
     36   
    3937 
    4038check_PROGRAMS = $(TESTS)
    … …  
    4644TESTSOURCES = \
    4745  ActOnAllUnitTest.cpp \
    48   ActionSequenceTest.cpp \
    4946  analysisbondsunittest.cpp \
    5047  AnalysisCorrelationToPointUnitTest.cpp \
    5148  AnalysisCorrelationToSurfaceUnitTest.cpp  \
    5249  AnalysisPairCorrelationUnitTest.cpp \
    53   AtomDescriptorTest.cpp \
    54   atomsCalculationTest.cpp \
    5550  bondgraphunittest.cpp \
    56   CacheableTest.cpp \
    57   DescriptorUnittest.cpp \
    5851  gslmatrixsymmetricunittest.cpp \
    5952  gslmatrixunittest.cpp \
    … …  
    6356  listofbondsunittest.cpp \
    6457  logunittest.cpp \
    65   manipulateAtomsTest.cpp \
    6658  memoryallocatorunittest.cpp  \
    6759  memoryusageobserverunittest.cpp \
    68   MoleculeDescriptorTest.cpp \
    69   ObserverTest.cpp \
    70   ParserUnitTest.cpp \
    7160  stackclassunittest.cpp \
    7261  tesselationunittest.cpp \
    7362  tesselation_boundarytriangleunittest.cpp \
    7463  tesselation_insideoutsideunittest.cpp \
    75   vectorunittest.cpp
     64  vectorunittest.cpp \
     65  ObserverTest.cpp \
     66  CacheableTest.cpp \
     67  DescriptorUnittest.cpp \
     68  ParserUnitTest.cpp \
     69  manipulateAtomsTest.cpp \
     70  atomsCalculationTest.cpp \
     71  ActionSequenceTest.cpp
    7672
    7773TESTHEADERS = \
    … …  
    123119MemoryUsageObserverUnitTest_LDADD = ${ALLLIBS}
    124120
    125 MoleculeDescriptorTest_SOURCES = UnitTestMain.cpp MoleculeDescriptorTest.cpp MoleculeDescriptorTest.hpp
    126 MoleculeDescriptorTest_LDADD = ${ALLLIBS}
    127 
    128121StackClassUnitTest_SOURCES = UnitTestMain.cpp stackclassunittest.cpp stackclassunittest.hpp
    129122StackClassUnitTest_LDADD = ${ALLLIBS}
    … …  
    150143CacheableTest_LDADD = ${ALLLIBS}
    151144
    152 AtomDescriptorTest_SOURCES = UnitTestMain.cpp AtomDescriptorTest.cpp AtomDescriptorTest.hpp
    153 AtomDescriptorTest_LDADD = ${ALLLIBS}
     145DescriptorUnittest_SOURCES = UnitTestMain.cpp DescriptorUnittest.cpp DescriptorUnittest.hpp
     146DescriptorUnittest_LDADD = ${ALLLIBS}
    154147
    155148ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp

  • src/unittests/atomsCalculationTest.cpp

    rcb2146 r7dc102  
    3030class AtomStub : public atom {
    3131public:
    32   AtomStub(atomId_t _id) :
     32  AtomStub(int _id) :
    3333  atom(),
    3434  id(_id),
    … …  
    3636  {}
    3737
    38   virtual atomId_t getId(){
     38  virtual int getId(){
    3939    return id;
    4040  }
    … …  
    4646  bool manipulated;
    4747private:
    48   atomId_t id;
     48  int id;
    4949};
    5050

  • src/unittests/manipulateAtomsTest.cpp

    rcb2146 r7dc102  
    3434  {}
    3535
    36   virtual atomId_t getId(){
     36  virtual int getId(){
    3737    return id;
    3838  }
    … …  
    4444  bool manipulated;
    4545private:
    46   atomId_t id;
     46  int id;
    4747};
    4848
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