# begin_html
# <b>Up:</b> <a href="index.html">Index</a>
# end_html

MAXILL_LNFLAGS = $(LNFLAGS) -shared -fPIC -lm -g $(OPENMPFLAGS) $(OPENMPLINK) $(OPENCLLINK) -L. -lqubfast

MAXILL_SRCFILES := $(shell find qubx_single_molecule -mindepth 1 -maxdepth 3 -name "*.cpp")
MAXILL_HDRFILES := $(shell find qubx_single_molecule -mindepth 1 -maxdepth 3 -name "*.h")
MAXILL_HTMLFILES := $(shell find $(APIDIR)/qubx_single_molecule -mindepth 1 -maxdepth 3 -name "*.html")
MAXILL_OBJFILES := $(patsubst %.cpp,$(OBJDIR)/%.o,$(MAXILL_SRCFILES))
MAXILL_AUXFILES := $(shell find qubx_single_molecule -mindepth 1 -maxdepth 3 -name "*.txt")
MAXILL_AUXFILES += qubx_single_molecule/Makefile_qubx_single_molecule.in qubx_single_molecule/make_deb.sh \
                   qubx_single_molecule/maxill.sln qubx_single_molecule/maxill.vcproj \
                   qubx_single_molecule/qubx_single_molecule.nsi
MAXILL_PYFILES := $(shell find qubx_single_molecule -mindepth 1 -maxdepth 3 -name "*.py")
MAXILL_PLUGFILES := $(MAXILL_SRCFILES) $(MAXILL_HDRFILES) $(MAXILL_AUXFILES) $(MAXILL_PYFILES)
MAXILL_ALLFILES := $(MAXILL_PLUGFILES) $(MAXILL_HTMLFILES)

SRCFILES += $(MAXILL_SRCFILES)
HDRFILES += $(MAXILL_HDRFILES)
HTMLFILES += $(MAXILL_HTMLFILES)
OBJFILES += $(MAXILL_OBJFILES)
AUXFILES += $(MAXILL_AUXFILES)
PYFILES += $(MAXILL_PYFILES)
PY_PACKAGEDIRS += qubx_single_molecule/qubx_single

qubx_single_molecule: libmaxill$(OPENCLEXT).so maxill_zip

qubx_single_molecule_test: libmaxill$(OPENCLEXT).so $(MAXILL_ALLFILES)

qubx_single_molecule_clean:
	-@rm  $(wildcard $(MAXILL_OBJFILES) libmaxill$(OPENCLEXT).so)

qubx_single_molecule_install: maxill_install maxill_zip
	-@mkdir -p /usr/share/qub-express/Plugins
	rsync -a $(APIDIR)/qubx_single_molecule /usr/share/qub-express/Plugins

qubx_single_molecule_install_local: maxill_install_local maxill_zip
	-@mkdir -p $(HOME)/.qub-express/Plugins
	rsync -a qubx_single_molecule $(HOME)/.qub-express/Plugins

maxill_install: libmaxill$(OPENCLEXT).so
	cp libmaxill$(OPENCLEXT).so /usr/lib

maxill_install_local: libmaxill$(OPENCLEXT).so
	-@mkdir -p $(HOME)/.local/lib
	cp libmaxill$(OPENCLEXT).so $(HOME)/.local/lib

$(OBJDIR)/qubx_single_molecule/max_subi_ll.d $(OBJDIR)/qubx_single_molecule/max_subi_ll.o: \
 qubx_single_molecule/max_subi_ll.cpp qubx_single_molecule/max_subi_ll.h \
  qubx_single_molecule/maxill.h common/callbk_reportfun.h \
  qubx_single_molecule/../qubfast/qubx_model.h \
  qubx_single_molecule/../qubfast/qubfast.h common/callbk_reportfun.h \
  qubx_single_molecule/max_inter_ll.h \
  qubx_single_molecule/../qubfast/max_ll_util.h \
  qubx_single_molecule/../qubfast/ublas_plus.h \
  qubx_single_molecule/../qubfast/ublas_matrixutil.h \
  qubx_single_molecule/../qubfast/matrixutil.h \
  qubx_single_molecule/../qubfast/milutil.h common/matrix.h \
  qubx_single_molecule/../qubfast/callbk_reportstream.h \
  qubx_single_molecule/max_subi_ll.opencl
	mkdir -p $(OBJDIR)/qubx_single_molecule
	$(CCP) $(CFLAGS) $(OPENMPFLAGS) $(OPENCLFLAGS) -MMD -MP -MT "$(OBJDIR)/qubx_single_molecule/max_subi_ll.d $(OBJDIR)/qubx_single_molecule/max_subi_ll.o" -c qubx_single_molecule/max_subi_ll.cpp -o $(OBJDIR)/qubx_single_molecule/max_subi_ll.o

obj/qubx_single_molecule/qubx_idealize.d obj/qubx_single_molecule/qubx_idealize.o: \
 qubx_single_molecule/qubx_idealize.cpp \
 qubx_single_molecule/qubx_idealize.h qubx_single_molecule/maxill.h \
 qubx_single_molecule/../qubfast/qubx_model.h \
 qubx_single_molecule/../qubfast/qubfast.h common/callbk_reportfun.h \
 qubx_single_molecule/../qubfast/max_ll_util.h \
 qubx_single_molecule/../qubfast/ublas_plus.h \
 qubx_single_molecule/../qubfast/ublas_matrixutil.h \
 qubx_single_molecule/../qubfast/matrixutil.h \
 qubx_single_molecule/../qubfast/milutil.h common/matrix.h \
 qubx_single_molecule/../qubfast/callbk_reportstream.h \
 qubx_single_molecule/../qubfast/running_mean.h \
 qubx_single_molecule/../qubfast/sampled_gaussian.h \
 qubx_single_molecule/../qubfast/qub_constraints.h \
 qubx_single_molecule/../qubfast/nmsimplex.h \
 qubx_single_molecule/../qubfast/qubx_model_storage.h \
 qubx_single_molecule/../qubfast/qubx_model.h \
 qubx_single_molecule/../qubfast/callbk_reportstream.h \
 qubx_single_molecule/../qubfast/qub_kalman.h
	mkdir -p $(OBJDIR)/qubx_single_molecule
	$(CCP) $(CFLAGS) $(OPENMPFLAGS) -MMD -MP -MT "$(OBJDIR)/qubx_single_molecule/qubx_idealize.d $(OBJDIR)/qubx_single_molecule/qubx_idealize.o" -c qubx_single_molecule/qubx_idealize.cpp -o $(OBJDIR)/qubx_single_molecule/qubx_idealize.o

qubx_single_molecule_docs: maxill_zip $(MAXILL_HTMLFILES)
	cp -a $(MAXILL_AUXFILES) $(APIDIR)/qubx_single_molecule/

libmaxill$(OPENCLEXT).so:	$(MAXILL_OBJFILES) $(COMMON_OBJFILES) libqubfast.so
	$(LN) -o libmaxill$(OPENCLEXT).so $(MAXILL_OBJFILES) $(COMMON_OBJFILES) $(MAXILL_LNFLAGS) 

maxill_zip: qubx_single_molecule_test py_docs
	@rsync -avR $(MAXILL_ALLFILES) $(TMPDIR)/
	@mkdir -p $(APIDIR)/qubx_single_molecule
	-@rsync -av $(APIDIR)/qubx_single_molecule/ $(APIDIR)/*qubx_single[.-]* $(TMPDIR)/qubx_single_molecule/
	-@rm $(TMPDIR)/qubx_single_molecule/qubx_single_molecule.zip
	@sh -c 'cd $(TMPDIR); zip -r qubx_single_molecule.zip qubx_single_molecule'
	mv $(TMPDIR)/qubx_single_molecule.zip $(APIDIR)/qubx_single_molecule

maxill_deb: $(MAXILL_ALLFILES) libmaxill$(OPENCLEXT).so
	-@rm -fr $(TMPDIR)/qubx_single_molecule-deb
	-@mkdir -p $(TMPDIR)/qubx_single_molecule-deb/usr/lib
	@cp -a libmaxill*.so $(TMPDIR)/qubx_single_molecule-deb/usr/lib
	-@mkdir -p $(TMPDIR)/qubx_single_molecule-deb/usr/share/qub-express/Plugins
	@rsync -avR $(MAXILL_PLUGFILES) $(TMPDIR)/qubx_single_molecule-deb/usr/share/qub-express/Plugins/
	qubx_single_molecule/make_deb.sh $(DISTRO) release $(TMPDIR)/qubx_single_molecule-deb
#	qubx_single_molecule/make_deb.sh none release $(TMPDIR)/qubx_single_molecule-deb

maxill_deb_other: $(MAXILL_ALLFILES) libmaxill$(OPENCLEXT).so
	-@rm -fr $(TMPDIR)/qubx_single_molecule-deb
	-@mkdir -p $(TMPDIR)/qubx_single_molecule-deb/usr/lib
	@cp -a libmaxill*.so $(TMPDIR)/qubx_single_molecule-deb/usr/lib
	-@mkdir -p $(TMPDIR)/qubx_single_molecule-deb/usr/share/qub-express/Plugins
	@rsync -avR $(MAXILL_PLUGFILES) $(TMPDIR)/qubx_single_molecule-deb/usr/share/qub-express/Plugins/
	qubx_single_molecule/make_deb.sh other release $(TMPDIR)/qubx_single_molecule-deb