# PKG_CXXFLAGS+= -I../RcppSrc -I./imslib/src/
# PKG_LIBS+= -L../RcppSrc -lRcpp 

PKG_CXXFLAGS+= -I./imslib/src/

PKG_LIBS=`${R_HOME}/bin/Rscript -e "RcppClassic:::LdFlags()" ` `${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"` 


.PHONY: all
all: $(SHLIB) 

IMSOBJECTS=imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o

DISOPOBJECTS=disop.o

OBJECTS=$(DISOPOBJECTS) $(IMSOBJECTS)

imslib/src/ims/element.o: imslib/src/ims/element.cpp 
imslib/src/ims/composedelement.o: imslib/src/ims/composedelement.cpp
imslib/src/ims/isotopedistribution.o: imslib/src/ims/isotopedistribution.cpp
imslib/src/ims/alphabet.o: imslib/src/ims/alphabet.cpp
imslib/src/ims/weights.o: imslib/src/ims/weights.cpp
imslib/src/ims/distributedalphabet.o: imslib/src/ims/distributedalphabet.cpp
imslib/src/ims/transformation.o: imslib/src/ims/transformation.cpp
imslib/src/ims/isotopespecies.o: imslib/src/ims/isotopespecies.cpp
imslib/src/ims/base/parser/alphabettextparser.o: imslib/src/ims/base/parser/alphabettextparser.cpp
imslib/src/ims/base/parser/distributedalphabettextparser.o: imslib/src/ims/base/parser/distributedalphabettextparser.cpp
imslib/src/ims/base/parser/massestextparser.o: imslib/src/ims/base/parser/massestextparser.cpp
imslib/src/ims/base/parser/moleculesequenceparser.o: imslib/src/ims/base/parser/moleculesequenceparser.cpp
imslib/src/ims/base/parser/standardmoleculesequenceparser.o: imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp
imslib/src/ims/base/parser/keggligandcompoundsparser.o: imslib/src/ims/base/parser/keggligandcompoundsparser.cpp
imslib/src/ims/base/parser/moleculeionchargemodificationparser.o: imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp
imslib/src/ims/calib/linepairstabber.o: imslib/src/ims/calib/linepairstabber.cpp
imslib/src/ims/calib/matchmatrix.o: imslib/src/ims/calib/matchmatrix.cpp
imslib/src/ims/calib/linearpointsetmatcher.o: imslib/src/ims/calib/linearpointsetmatcher.cpp
imslib/src/ims/decomp/realmassdecomposer.o: imslib/src/ims/decomp/realmassdecomposer.cpp
imslib/src/ims/utils/distribution.o: imslib/src/ims/utils/distribution.cpp
imslib/src/ims/distributionprobabilityscorer.o: imslib/src/ims/distributionprobabilityscorer.cpp
imslib/src/ims/characteralphabet.o: imslib/src/ims/characteralphabet.cpp
imslib/src/ims/nitrogenrulefiltero: imslib/src/ims/nitrogenrulefilter.cp

clean:
	$(MAKE) -C imslib clean
	rm -f $(OBJECTS)