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

SUBDIRS = Actions Exceptions LinearAlgebra Parser UIElements

AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}

ATOMSOURCE = \
  atom.cpp \
  AtomicInfo.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 \
  AtomicInfo.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

ANALYSISSOURCE = \
  analysis_bonds.cpp \
  analysis_correlation.cpp
ANALYSISHEADER = \
  analysis_bonds.hpp \
  analysis_correlation.hpp

ACTIONSSOURCE = \
  Actions/Action.cpp \
  Actions/ActionHistory.cpp \
  Actions/ActionRegistry.cpp \
  Actions/ActionSequence.cpp \
  Actions/ActionTraits.cpp \
  Actions/ErrorAction.cpp \
  Actions/MakroAction.cpp \
  Actions/ManipulateAtomsProcess.cpp \
  Actions/MethodAction.cpp \
	Actions/OptionRegistry.cpp \
	Actions/OptionTrait.cpp \
  Actions/Process.cpp

ACTIONSHEADER = \
  Actions/Action.hpp \
  Actions/ActionHistory.hpp \
  Actions/ActionRegistry.hpp \
  Actions/ActionSequence.hpp \
  Actions/ActionTraits.hpp \
  Actions/Calculation.hpp \
  Actions/Calculation_impl.hpp \
  Actions/ErrorAction.hpp \
  Actions/MakroAction.hpp \
  Actions/ManipulateAtomsProcess.hpp \
  Actions/MethodAction.hpp \
	Actions/OptionRegistry.hpp \
	Actions/OptionTrait.hpp \
  Actions/Process.hpp


SHAPESOURCE = \
  Shapes/BaseShapes.cpp \
  Shapes/Shape.cpp \
  Shapes/ShapeOps.cpp
SHAPEHEADER = \
  Shapes/BaseShapes.hpp \
  Shapes/Shape.hpp \
  Shapes/ShapeOps.hpp

  
DESCRIPTORSOURCE = \
	Descriptors/AtomDescriptor.cpp \
  Descriptors/AtomIdDescriptor.cpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor.cpp \
  Descriptors/AtomSelectionDescriptor.cpp \
  Descriptors/AtomShapeDescriptor.cpp \
  Descriptors/AtomTypeDescriptor.cpp \
  Descriptors/MoleculeDescriptor.cpp \
  Descriptors/MoleculeFormulaDescriptor.cpp \
  Descriptors/MoleculeIdDescriptor.cpp \
  Descriptors/MoleculeNameDescriptor.cpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor.cpp \
  Descriptors/MoleculeOrderDescriptor.cpp \
  Descriptors/MoleculePtrDescriptor.cpp \
  Descriptors/MoleculeSelectionDescriptor.cpp
				   

DESCRIPTORHEADER = \
	Descriptors/AtomDescriptor.hpp \
  Descriptors/AtomIdDescriptor.hpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor.hpp \
  Descriptors/AtomSelectionDescriptor.hpp \
  Descriptors/AtomShapeDescriptor.hpp \
  Descriptors/AtomTypeDescriptor.hpp \
  Descriptors/MoleculeDescriptor.hpp \
  Descriptors/MoleculeFormulaDescriptor.hpp \
  Descriptors/MoleculeIdDescriptor.hpp \
  Descriptors/MoleculeNameDescriptor.hpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor.hpp \
  Descriptors/MoleculeOrderDescriptor.hpp \
  Descriptors/MoleculePtrDescriptor.hpp \
  Descriptors/MoleculeSelectionDescriptor.hpp
  
DESCRIPTORIMPLHEADER = \
	Descriptors/AtomDescriptor_impl.hpp \
  Descriptors/AtomIdDescriptor_impl.hpp \
  Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp \
  Descriptors/AtomSelectionDescriptor_impl.hpp \
  Descriptors/AtomShapeDescriptor_impl.hpp \
  Descriptors/AtomTypeDescriptor_impl.hpp \
  Descriptors/MoleculeDescriptor_impl.hpp \
  Descriptors/MoleculeFormulaDescriptor_impl.hpp \
  Descriptors/MoleculeIdDescriptor_impl.hpp \
  Descriptors/MoleculeNameDescriptor_impl.hpp \
  Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp \
  Descriptors/MoleculeOrderDescriptor_impl.hpp \
  Descriptors/MoleculePtrDescriptor_impl.hpp \
  Descriptors/MoleculeSelectionDescriptor_impl.hpp
  
THERMOSTATSOURCE = \
  Thermostats/Berendsen.cpp \
  Thermostats/GaussianThermostat.cpp \
  Thermostats/Langevin.cpp \
  Thermostats/NoseHoover.cpp \
  Thermostats/NoThermostat.cpp \
  Thermostats/Thermostat.cpp \
  Thermostats/Woodcock.cpp

THERMOSTATHEADER = \
  Thermostats/Berendsen.hpp \
  Thermostats/GaussianThermostat.hpp \
  Thermostats/Langevin.hpp \
  Thermostats/NoseHoover.hpp \
  Thermostats/NoThermostat.hpp \
  Thermostats/Thermostat.hpp \
  Thermostats/Woodcock.hpp

TESSELATIONSOURCE = \
  BoundaryLineSet.cpp \
  BoundaryPointSet.cpp \
  BoundaryPolygonSet.cpp \
  BoundaryTriangleSet.cpp \
  CandidateForTesselation.cpp \
  PointCloud.cpp \
  tesselation.cpp \
  tesselationhelpers.cpp \
  TesselPoint.cpp
  
TESSELATIONHEADER = \
  BoundaryLineSet.hpp \
  BoundaryPointSet.hpp \
  BoundaryPolygonSet.hpp \
  BoundaryTriangleSet.hpp \
  CandidateForTesselation.hpp \
  PointCloud.hpp \
  tesselation.hpp \
  tesselationhelpers.hpp \
  TesselPoint.hpp

MOLECUILDERSOURCE = \
  ${ANALYSISSOURCE} \
  ${ACTIONSSOURCE} \
  ${ATOMSOURCE} \
  ${PATTERNSOURCE} \
  ${SHAPESOURCE} \
  ${DESCRIPTORSOURCE} \
  ${THERMOSTATSOURCE} \
  ${TESSELATIONSOURCE} \
  Helpers/defs.cpp \
  Helpers/helpers.cpp \
  bond.cpp \
  bondgraph.cpp \
  boundary.cpp \
  Box.cpp \
  config.cpp \
  ConfigFileBuffer.cpp \
  element.cpp \
  elements_db.cpp \
  ellipsoid.cpp \
  Formula.cpp \
  graph.cpp \
  linkedcell.cpp \
  moleculelist.cpp \
  molecule.cpp \
  molecule_dynamics.cpp \
  molecule_fragmentation.cpp \
  molecule_geometry.cpp \
  molecule_graph.cpp \
  molecule_pointcloud.cpp \
  parser.cpp \
  periodentafel.cpp \
  ThermoStatContainer.cpp \
  triangleintersectionlist.cpp \
  UIElements/UIFactory.cpp \
  World.cpp

MOLECUILDERHEADER = \
  ${ANALYSISHEADER} \
  ${ACTIONSHEADER} \
  ${ATOMHEADER} \
  ${PATTERNHEADER} \
  ${SHAPEHEADER} \
  ${DESCRIPTORHEADER} \
  ${DESCRIPTORIMPLHEADER} \
  ${THERMOSTATHEADER} \
  ${TESSELATIONHEADER} \
  Helpers/defs.hpp \
  Helpers/fast_functions.hpp \
  Helpers/helpers.hpp \
  bond.hpp \
  bondgraph.hpp \
  boundary.hpp \
  Box.hpp \
  config.hpp \
  ConfigFileBuffer.hpp \
  element.hpp \
  elements_db.hpp \
  ellipsoid.hpp \
  Formula.hpp \
  graph.hpp \
  linkedcell.hpp \
  lists.hpp \
  molecule.hpp \
  parser.hpp \
  periodentafel.hpp \
  ThermoStatContainer.hpp \
  triangleintersectionlist.hpp \
  UIElements/UIFactory.hpp \
  World.hpp 

lib_LTLIBRARIES = libMolecuilder-@MOLECUILDER_API_VERSION@.la
libMolecuilder_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
libMolecuilder_LIBS = \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	${BOOST_PROGRAM_OPTIONS_LIB}

#	UIElements/libMolecuilderUI.a \
	Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
	Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
	$(BOOST_LIB) \
	${BOOST_THREAD_LIB}

nobase_libMolecuilder_include_HEADERS = ${MOLECUILDERHEADER}

## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
## will therefore be treated as if it were literally part of the target name,
## and the variable name derived from that.
## The file extension .cc is recognized by Automake, and makes it produce
## rules which invoke the C++ compiler to produce a libtool object file (.lo)
## from each source file.  Note that it is not necessary to list header files
## which are already listed elsewhere in a _HEADERS variable assignment.
libMolecuilder_@MOLECUILDER_API_VERSION@_la_SOURCES = ${MOLECUILDERSOURCE} $(srcdir)/version.c

## Instruct libtool to include ABI version information in the generated shared
## library file (.so).  The library ABI version is defined in configure.ac, so
## that all version information is kept in one place.
libMolecuilder_@MOLECUILDER_API_VERSION@_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)

## The generated configuration header is installed in its own subdirectory of
## $(libdir).  The reason for this is that the configuration information put
## into this header file describes the target platform the installed library
## has been built for.  Thus the file must not be installed into a location
## intended for architecture-independent files, as defined by the Filesystem
## Hierarchy Standard (FHS).
## The nodist_ prefix instructs Automake to not generate rules for including
## the listed files in the distribution on 'make dist'.  Files that are listed
## in _HEADERS variables are normally included in the distribution, but the
## configuration header file is generated at configure time and should not be
## shipped with the source tarball.
libMolecuilder_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
nodist_libMolecuilder_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h

## Install the generated pkg-config file (.pc) into the expected location for
## architecture-dependent package configuration information.  Occasionally,
## pkg-config files are also used for architecture-independent data packages,
## in which case the correct install location would be $(datadir)/pkgconfig.
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc


BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_FILESYSTEM_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_THREAD_LIB)
INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements

noinst_LIBRARIES = libmenu.a
bin_PROGRAMS = molecuilder molecuildergui joiner analyzer SubspaceFactorizer
EXTRA_PROGRAMS = unity

molecuilderdir = ${bindir}

libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER} 

molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db

SubspaceFactorizer_CXXFLAGS = $(BOOST_CPPFLAGS)
SubspaceFactorizer_SOURCES = SubspaceFactorizer.cpp Helpers/defs.cpp Helpers/defs.hpp Helpers/helpers.cpp Helpers/helpers.hpp
SubspaceFactorizer_LDADD = \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	$(GSLLIB) \
	$(BOOST_LIB)

molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
#molecuilder_CXXFLAGS += -DNO_CACHING
molecuilder_LDFLAGS = $(BOOST_LIB)
molecuilder_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
molecuilder_LDADD = \
	UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
	Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
	libMolecuilder-@MOLECUILDER_API_VERSION@.la \
	Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	$(BOOST_LIB)

#Stuff for building the GUI using Qt
molecuildergui_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
molecuildergui_CXXFLAGS = $(BOOST_CPPFLAGS) -DUSE_GUI_QT
molecuildergui_LDFLAGS = $(BOOST_LIB)

unity_SOURCES = unity.cpp
unity_LDADD = $(BOOST_LIB)

molecuildergui_LDADD = \
	UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
	UIElements/libMolecuilderQtUI-@MOLECUILDER_API_VERSION@.la \
	Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
	libMolecuilder-@MOLECUILDER_API_VERSION@.la \
	Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	$(BOOST_LIB) \
	${GUI_LIBS}

joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
joiner_LDADD = \
	UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
	Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
	libMolecuilder-@MOLECUILDER_API_VERSION@.la \
	Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	$(BOOST_LIB)

analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp 
analyzer_LDADD = \
	UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
	Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
	libMolecuilder-@MOLECUILDER_API_VERSION@.la \
	Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
	LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
	Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
	${CodePatterns_LIBS} \
	$(BOOST_LIB)

#EXTRA_DIST = ${molecuilder_DATA}

FORCE:
$(srcdir)/.git-version: FORCE
	@if (test -d $(top_srcdir)/.git && cd $(srcdir) \
	     && { git describe --dirty --always || git describe; } ) > .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: $(srcdir)/.git-version
	echo "const char *MOLECUILDERVERSION = \"$(PACKAGE_NAME) version "`cat $(srcdir)/.git-version`"\";" > $@


unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
	echo "#include \"$(srcdir)/Helpers/MemDebug.cpp\"" >  unity.cpp; \
	list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
  	echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
	done; \
	subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
		olddir=$$PWD;\
		cd $$directory && make unity.cpp;\
		cd $$olddir;\
		echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
	done;\
	echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
	echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;

MOSTLYCLEANFILES = unity.cpp