# PLEASE adhere to the alphabetical ordering in this Makefile!
# Also indentation by a single tab

# this includes source files that need to be present at multiple points
HELPERSOURCE =  \
  Helpers/Assert.cpp \
  Helpers/MemDebug.cpp
		        
ATOMSOURCE = \
  atom.cpp \
  atom_atominfo.cpp \
  atom_bondedparticle.cpp \
  atom_bondedparticleinfo.cpp \
  atom_graphnode.cpp \
  atom_graphnodeinfo.cpp \
  atom_particleinfo.cpp \
  atom_trajectoryparticle.cpp \
  atom_trajectoryparticleinfo.cpp
ATOMHEADER = \
  atom.hpp \
  atom_atominfo.hpp \
  atom_bondedparticle.hpp \
  atom_bondedparticleinfo.hpp \
  atom_graphnode.hpp \
  atom_graphnodeinfo.hpp \
  atom_particleinfo.hpp \
  atom_trajectoryparticle.hpp \
  atom_trajectoryparticleinfo.hpp

LINALGSOURCE = \
  ${HELPERSOURCE} \
  gslmatrix.cpp \
  gslvector.cpp \
  linearsystemofequations.cpp \
  Space.cpp \
  vector.cpp
			   
LINALGHEADER = gslmatrix.hpp \
  gslvector.hpp \
  linearsystemofequations.hpp \
  Space.hpp \
  vector.hpp
			   
ANALYSISSOURCE = \
  analysis_bonds.cpp \
  analysis_correlation.cpp
ANALYSISHEADER = \
  analysis_bonds.hpp \
  analysis_correlation.hpp

ACTIONSSOURCE = Actions/Action.cpp \
  ${ANALYSISACTIONSOURCE} \
  ${ATOMACTIONSOURCE} \
  ${CMDACTIONSOURCE} \
  ${FRAGMENTATIONACTIONSOURCE} \
  ${MOLECULEACTIONSOURCE} \
  ${PARSERACTIONSOURCE} \
  ${TESSELATIONACTIONSOURCE} \
  ${WORLDACTIONSOURCE} \
  Actions/ActionHistory.cpp \
  Actions/ActionRegistry.cpp \
  Actions/ActionSequence.cpp \
  Actions/ErrorAction.cpp \
  Actions/MakroAction.cpp \
  Actions/ManipulateAtomsProcess.cpp \
  Actions/MapOfActions.cpp \
  Actions/MethodAction.cpp \
  Actions/Process.cpp

ACTIONSHEADER = Actions/Action.hpp \
  ${ANALYSISACTIONHEADER} \
  ${ATOMACTIONHEADER} \
  ${CMDACTIONHEADER} \
  ${FRAGMENTATIONACTIONHEADER} \
  ${MOLECULEACTIONHEADER} \
  ${PARSERACTIONHEADER} \
  ${TESSELATIONACTIONHEADER} \
  ${WORLDACTIONHEADER} \
  Actions/ActionHistory.hpp \
  Actions/ActionRegistry.hpp \
  Actions/ActionSequence.hpp \
  Actions/Calculation.hpp \
  Actions/Calculation_impl.hpp \
  Actions/ErrorAction.hpp \
  Actions/MakroAction.hpp \
  Actions/ManipulateAtomsProcess.hpp \
  Actions/MapOfActions.hpp \
  Actions/MethodAction.hpp \
  Actions/Process.hpp
  
ANALYSISACTIONSOURCE = \
  Actions/AnalysisAction/MolecularVolumeAction.cpp \
  Actions/AnalysisAction/PairCorrelationAction.cpp \
  Actions/AnalysisAction/PairCorrelationToPointAction.cpp \
  Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp \
  Actions/AnalysisAction/PrincipalAxisSystemAction.cpp
ANALYSISACTIONHEADER = \
  Actions/AnalysisAction/MolecularVolumeAction.hpp \
  Actions/AnalysisAction/PairCorrelationAction.hpp \
  Actions/AnalysisAction/PairCorrelationToPointAction.hpp \
  Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp \
  Actions/AnalysisAction/PrincipalAxisSystemAction.hpp

ATOMACTIONSOURCE = \
  Actions/AtomAction/AddAction.cpp \
  Actions/AtomAction/ChangeElementAction.cpp \
  Actions/AtomAction/RemoveAction.cpp
ATOMACTIONHEADER = \
  Actions/AtomAction/AddAction.hpp \
  Actions/AtomAction/ChangeElementAction.hpp \
  Actions/AtomAction/RemoveAction.cpp

CMDACTIONSOURCE = \
  Actions/CmdAction/BondLengthTableAction.cpp \
  Actions/CmdAction/ElementDbAction.cpp \
  Actions/CmdAction/FastParsingAction.cpp \
  Actions/CmdAction/HelpAction.cpp \
  Actions/CmdAction/VerboseAction.cpp \
  Actions/CmdAction/VersionAction.cpp
CMDACTIONHEADER = \
  Actions/CmdAction/BondLengthTableAction.hpp \
  Actions/CmdAction/ElementDbAction.hpp \
  Actions/CmdAction/FastParsingAction.hpp \
  Actions/CmdAction/HelpAction.hpp \
  Actions/CmdAction/VerboseAction.hpp \
  Actions/CmdAction/VersionAction.hpp

FRAGMENTATIONACTIONSOURCE = \
  Actions/FragmentationAction/DepthFirstSearchAction.cpp \
  Actions/FragmentationAction/FragmentationAction.cpp \
  Actions/FragmentationAction/SubgraphDissectionAction.cpp               
FRAGMENTATIONACTIONHEADER = \
  Actions/FragmentationAction/DepthFirstSearchAction.hpp \
  Actions/FragmentationAction/FragmentationAction.hpp \
  Actions/FragmentationAction/SubgraphDissectionAction.hpp

MOLECULEACTIONSOURCE = \
  Actions/MoleculeAction/BondFileAction.cpp \
  Actions/MoleculeAction/ChangeNameAction.cpp \
  Actions/MoleculeAction/FillWithMoleculeAction.cpp \
  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
  Actions/MoleculeAction/SaveAdjacencyAction.cpp \
  Actions/MoleculeAction/SaveBondsAction.cpp \
  Actions/MoleculeAction/SaveTemperatureAction.cpp \
  Actions/MoleculeAction/SuspendInWaterAction.cpp \
  Actions/MoleculeAction/TranslateAction.cpp \
  Actions/MoleculeAction/VerletIntegrationAction.cpp
MOLECULEACTIONHEADER = \
  Actions/MoleculeAction/BondFileAction.hpp \
  Actions/MoleculeAction/ChangeNameAction.hpp \
  Actions/MoleculeAction/FillWithMoleculeAction.hpp \
  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
  Actions/MoleculeAction/SaveAdjacencyAction.hpp \
  Actions/MoleculeAction/SaveBondsAction.hpp \
  Actions/MoleculeAction/SaveTemperatureAction.hpp \
  Actions/MoleculeAction/SuspendInWaterAction.hpp \
  Actions/MoleculeAction/TranslateAction.hpp \
  Actions/MoleculeAction/VerletIntegrationAction.hpp
                 
PARSERACTIONSOURCE = \
  Actions/ParserAction/LoadXyzAction.cpp \
  Actions/ParserAction/SaveXyzAction.cpp       
PARSERACTIONHEADER = \
  Actions/ParserAction/LoadXyzAction.hpp \
  Actions/ParserAction/SaveXyzAction.hpp

TESSELATIONACTIONSOURCE = \
  Actions/TesselationAction/ConvexEnvelopeAction.cpp \
  Actions/TesselationAction/NonConvexEnvelopeAction.cpp               
TESSELATIONACTIONHEADER = \
  Actions/TesselationAction/ConvexEnvelopeAction.hpp \
  Actions/TesselationAction/NonConvexEnvelopeAction.hpp

WORLDACTIONSOURCE = \
  Actions/WorldAction/AddEmptyBoundaryAction.cpp \
  Actions/WorldAction/BoundInBoxAction.cpp \
  Actions/WorldAction/CenterInBoxAction.cpp \
  Actions/WorldAction/CenterOnEdgeAction.cpp \
  Actions/WorldAction/ChangeBoxAction.cpp \
  Actions/WorldAction/RemoveSphereOfAtomsAction.cpp \
  Actions/WorldAction/RepeatBoxAction.cpp \
  Actions/WorldAction/ScaleBoxAction.cpp \
  Actions/WorldAction/SetDefaultNameAction.cpp \
  Actions/WorldAction/SetGaussianBasisAction.cpp               
WORLDACTIONHEADER = \
  Actions/WorldAction/AddEmptyBoundaryAction.hpp \
  Actions/WorldAction/BoundInBoxAction.hpp \
  Actions/WorldAction/CenterInBoxAction.hpp \
  Actions/WorldAction/CenterOnEdgeAction.hpp \
  Actions/WorldAction/ChangeBoxAction.hpp \
  Actions/WorldAction/RemoveSphereOfAtomsAction.hpp \
  Actions/WorldAction/RepeatBoxAction.hpp \
  Actions/WorldAction/ScaleBoxAction.hpp \
  Actions/WorldAction/SetDefaultNameAction.hpp \
  Actions/WorldAction/SetGaussianBasisAction.hpp



PARSERSOURCE = \
  Parser/ChangeTracker.cpp \
  Parser/FormatParser.cpp \
  Parser/TremoloParser.cpp \
  Parser/XyzParser.cpp
PARSERHEADER = \
  Parser/ChangeTracker.hpp \
  Parser/FormatParser.hpp \
  Parser/TremoloParser.hpp \
  Parser/XyzParser.hpp

PATTERNSOURCE = \
  Patterns/Observer.cpp
PATTERNHEADER = \
  Patterns/Cacheable.hpp \
  Patterns/Observer.hpp \
  Patterns/Singleton.hpp

# Below is all for the User Interface

VIEWSOURCE = \
  Views/View.cpp \
  Views/StringView.cpp \
  Views/MethodStringView.cpp \
  Views/StreamStringView.cpp
VIEWHEADER = \
  Views/View.hpp \
  Views/StringView.hpp \
  Views/MethodStringView.hpp \
  Views/StreamStringView.hpp

MENUSOURCE = \
  Menu/Menu.cpp \
  Menu/TextMenu.cpp \
  Menu/MenuItem.cpp \
  Menu/SubMenuItem.cpp \
  Menu/ActionMenuItem.cpp \
  Menu/SeperatorItem.cpp \
  Menu/DisplayMenuItem.cpp
  
MENUHEADER = \
  Menu/Menu.hpp \
  Menu/TextMenu.hpp \
  Menu/MenuItem.hpp \
  Menu/SubMenuItem.hpp \
  Menu/ActionMenuItem.hpp \
  Menu/SeperatorItem.hpp \
  Menu/DisplayMenuItem.hpp

UISOURCE = \
  ${ACTIONSSOURCE} \
  ${COMMANDLINEUISOURCE} \
  ${MENUSOURCE} \
  ${TEXTUISOURCE} \
  ${VIEWSOURCE} \
  UIElements/Dialog.cpp \
  UIElements/MainWindow.cpp \
  UIElements/UIFactory.cpp
  
UIHEADER = \
  ${ACTIONSHEADER} \
  ${COMMANDLINEUIHEADER} \
  ${MENUHEADER} \
  ${TEXTUIHEADER} \
  ${VIEWHEADER} \
  UIElements/Dialog.hpp \
  UIElements/MainWindow.hpp \
  UIElements/UIFactory.hpp

TEXTUISOURCE = \
  UIElements/TextDialog.cpp \
  UIElements/TextStatusIndicator.cpp \
  UIElements/TextUIFactory.cpp \
  UIElements/TextWindow.cpp
TEXTUIHEADER = \
  UIElements/TextDialog.hpp \
  UIElements/TextStatusIndicator.hpp \
  UIElements/TextUIFactory.hpp \
  UIElements/TextWindow.hpp

COMMANDLINEUISOURCE = \
  UIElements/CommandLineDialog.cpp \
  UIElements/CommandLineStatusIndicator.cpp \
  UIElements/CommandLineUIFactory.cpp \
  UIElements/CommandLineWindow.cpp
COMMANDLINEUIHEADER = \
  UIElements/CommandLineDialog.hpp \
  UIElements/CommandLineStatusIndicator.hpp \
  UIElements/CommandLineUIFactory.hpp \
  UIElements/CommandLineWindow.hpp

# all these files are only used for legacy reasons while the transition is in progress
# they are only needed to keep the program usable at any point of the transition and will be 
# deleted once everything is fully refactored
LEGACYSOURCE = Legacy/oldmenu.cpp 
LEGACYHEADER = Legacy/oldmenu.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
				   
EXCEPTIONSOURCE = Exceptions/CustomException.cpp \
  Exceptions/LinearDependenceException.cpp \
  Exceptions/MathException.cpp \
  Exceptions/ZeroVectorException.cpp
				  
EXCEPTIONHEADER = Exceptions/CustomException.hpp \
  Exceptions/LinearDependenceException.hpp \
  Exceptions/MathException.hpp \
  Exceptions/ZeroVectorException.hpp

SOURCE = \
  ${ANALYSISSOURCE} \
  ${ATOMSOURCE} \
  ${PATTERNSOURCE} \
  ${PARSERSOURCE} \
  ${UISOURCE} \
  ${DESCRIPTORSOURCE} \
  ${HELPERSOURCE} \
  ${LEGACYSOURCE} \
  ${EXCEPTIONSOURCE} \
  bond.cpp \
  bondgraph.cpp \
  boundary.cpp \
  CommandLineParser.cpp \
  config.cpp \
  element.cpp \
  ellipsoid.cpp \
  errorlogger.cpp \
  graph.cpp \
  helpers.cpp \
  info.cpp \
  leastsquaremin.cpp \
  Line.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 \
  Plane.cpp \
  tesselation.cpp \
  tesselationhelpers.cpp \
  triangleintersectionlist.cpp \
  verbose.cpp \
  vector_ops.cpp \
  World.cpp

HEADER = \
  ${ANALYSISHEADER} \
  ${ATOMHEADER} \
  ${PARSERHEADER} \
  ${PATTERNHEADER} \
  ${UIHEADER} \
  ${DESCRIPTORHEADER} \
  ${EXCEPTIONHEADER} \
  ${LEGACYHEADER} \
  bond.hpp \
  bondgraph.hpp \
  boundary.hpp \
  CommandLineParser.hpp \
  config.hpp \
  defs.hpp \
  element.hpp \
  ellipsoid.hpp \
  errorlogger.hpp \
  graph.hpp \
  helpers.hpp \
  info.hpp \
  leastsquaremin.hpp \
  Line.hpp \
  linkedcell.hpp \
  lists.hpp \
  log.hpp \
  logger.hpp \
  memoryallocator.hpp \
  memoryusageobserver.hpp \
  molecule.hpp \
  molecule_template.hpp \
  parser.hpp \
  periodentafel.hpp \
  Plane.hpp \
  stackclass.hpp \
  tesselation.hpp \
  tesselationhelpers.hpp \
  triangleintersectionlist.hpp \
  verbose.hpp \
  vector_ops.hpp \
  World.hpp 

BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
INCLUDES = -I$(top_srcdir)/src/unittests

noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
bin_PROGRAMS = molecuilder joiner analyzer
molecuilderdir = ${bindir}
libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
molecuilder_SOURCES = builder.cpp
molecuilder_LDADD = libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp 
analyzer_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}

FORCE:
$(srcdir)/.git-version: FORCE
	@if (test -d $(top_srcdir)/../.git && cd $(srcdir) && git describe HEAD) > .git-version-t 2>/dev/null \
	  && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
	  mv -f .git-version-t $(srcdir)/.git-version; \
	else \
	  rm -f .git-version-t; \
	fi

EXTRA_DIST = $(srcdir)/.git-version

$(srcdir)/version.c: $(srcdir)/.git-version
	echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@

molecuilder_SOURCES += $(srcdir)/version.c