Changeset ab4b55 for src

Timestamp:

Mar 5, 2010, 12:53:13 PM (15 years ago)

Author:

Saskia Metzler <metzler@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

7dc102

Parents:

57f5cf

Message:

the XYZ parser

Location:

src

Files:

• FormatParser.cpp (deleted)
• Makefile.am (modified) (2 diffs)
• Matrix.cpp (deleted)
• Matrix.hpp (deleted)
• Parser/ChangeTracker.cpp (moved) (moved from src/ChangeTracker.cpp ) (4 diffs)
• Parser/ChangeTracker.hpp (moved) (moved from src/ChangeTracker.hpp )
• Parser/FormatParser.cpp (added)
• Parser/FormatParser.hpp (moved) (moved from src/FormatParser.hpp ) (1 diff)
• Parser/TremoloParser.cpp (moved) (moved from src/TremoloParser.cpp )
• Parser/TremoloParser.hpp (moved) (moved from src/TremoloParser.hpp )
• Parser/XyzParser.cpp (added)
• Parser/XyzParser.hpp (added)
• XyzParser.cpp (deleted)
• XyzParser.hpp (deleted)
• unittests/Makefile.am (modified) (3 diffs)
• unittests/MatrixUnitTest.cpp (deleted)
• unittests/MatrixUnitTest.hpp (deleted)
• unittests/ParserUnitTest.cpp (added)
• unittests/ParserUnitTest.hpp (added)

src/Makefile.am

@@ -10 +10 @@
 ACTIONSSOURCE = Actions/Action.cpp Actions/Process.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp Actions/small_actions.cpp Actions/ManipulateAtomsProcess.cpp Actions/ActionRegistry.cpp 
 ACTIONSHEADER = Actions/Action.hpp Actions/Process.hpp Actions/Calculation.hpp Actions/Calculation_impl.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp Actions/small_actions.hpp Actions/ManipulateAtomsProcess.hpp Actions/ActionRegistry.hpp
+
+PARSERSOURCE = Parser/ChangeTracker.cpp Parser/FormatParser.cpp Parser/XyzParser.cpp
+PARSERHEADER = Parser/ChangeTracker.hpp Parser/FormatParser.hpp Parser/XyzParser.hpp
 
 PATTERNSOURCE = Patterns/Observer.cpp
@@ -32 +35 @@
 DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp Descriptors/MoleculeDescriptor.hpp
 
-SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PATTERNSOURCE} ${UISOURCE} ${DESCRIPTORSOURCE} ${LEGACYSOURCE} bond.cpp bondgraph.cpp boundary.cpp ChangeTracker.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp FormatParser.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
-HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${PATTERNHEADER} ${UIHEADER} ${DESCRIPTORHEADER} ${LEGACYHEADER} bond.hpp bondgraph.hpp boundary.hpp ChangeTracker.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp FormatParser.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp World.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
+HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${PARSERHEADER} ${PATTERNHEADER} ${UIHEADER} ${DESCRIPTORHEADER} ${LEGACYHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp World.hpp
 
 BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

src/Parser/ChangeTracker.cpp

@@ -10 +10 @@
 ChangeTracker* ChangeTracker::instance = NULL;
 
+/**
+ * Constructor. Signs on as an observer for the World.
+ */
 ChangeTracker::ChangeTracker() {
   isConsistent = true;
@@ -15 +18 @@
 }
 
+/**
+ * Destructor. Signs off from the World.
+ */
 ChangeTracker::~ChangeTracker() {
   World::get()->signOff(this);
 }
 
+/**
+ * Returns the change tracker instance.
+ *
+ * \return this
+ */
 ChangeTracker* ChangeTracker::get() {
   if (instance == NULL) {
@@ -27 +38 @@
 }
 
+/**
+ * Destroys the change tracker instance. Be careful, the change tracker is a
+ * singleton and destruction might lead to a loss of consistency.
+ */
 void ChangeTracker::destroy() {
   delete instance;
@@ -32 +47 @@
 }
 
+/**
+ * With this, the World can update the change tracker's state.
+ */
 void ChangeTracker::update(Observable *publisher) {
   isConsistent = false;
 }
 
+/**
+ * Gets whether there are non-saved changes.
+ *
+ * \param true if there are any changes, false otherwise
+ */
 bool ChangeTracker::hasChanged() {
   return !isConsistent;
 }
 
+/**
+ * Tells all observers (which are the different parsers) that they are supposed
+ * to save the current state.
+ */
 void ChangeTracker::saveStatus() {
   if (hasChanged()) {

src/Parser/FormatParser.hpp

@@ -13 +13 @@
 #include "parser.hpp"
 
-using namespace std;
-
+/**
+ * General parser which observes the change tracker.
+ */
 class FormatParser : public Observer {
 public:
   FormatParser();
-  ~FormatParser();
-  virtual void save(char* fileName);
-  virtual void load(char* fileName);
+  virtual ~FormatParser();
+  virtual void save(std::ostream* file)=0;
+  virtual void load(std::istream* file)=0;
+  void setOstream(std::ostream* file);
+  void update(Observable *publisher);
+  void subjectKilled(Observable *publisher);
 
 private:
-  MatrixContainer* readData(char* fileName, int skiplines, int skipcolumns);
-  virtual int getHeaderSize(char identifier);
+  std::ostream* saveStream;
 };
 

src/unittests/Makefile.am

@@ -30 +30 @@
   CacheableTest \
   DescriptorUnittest \
-  MatrixUnitTest \
+  ParserUnitTest \
   manipulateAtomsTest \
   atomsCalculationTest \
@@ -66 +66 @@
   CacheableTest.cpp \
   DescriptorUnittest.cpp \
-  MatrixUnitTest.cpp \ 
+  ParserUnitTest.cpp \
   manipulateAtomsTest.cpp \
   atomsCalculationTest.cpp \
@@ -146 +146 @@
 DescriptorUnittest_LDADD = ${ALLLIBS}
 
-MatrixUnitTest_SOURCES = UnitTestMain.cpp MatrixUnitTest.cpp MatrixUnitTest.hpp
-MatrixUnitTest_LDADD = ${ALLLIBS}
+ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp
+ParserUnitTest_LDADD = ${ALLLIBS}
 
 manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp