all: $(SHLIB)

MYCXXFLAGS=-O1

%.o: %.cpp
	$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) $(MYCXXFLAGS) -c $< -o $@

PKG_CPPFLAGS+=\
 -imacros R_affx_constants.h\
 -Ifusion_sdk/calvin_files/data/src\
 -Ifusion_sdk/calvin_files/array/src\
 -Ifusion_sdk/calvin_files/portability/src\
 -Ifusion_sdk/calvin_files/utils/src\
 -Ifusion_sdk/calvin_files/exception/src\
 -Ifusion_sdk/calvin_files/parameter/src\
 -Ifusion_sdk/calvin_files/parsers/src\
 -Ifusion_sdk/calvin_files/template/src\
 -Ifusion_sdk/file\
 -Ifusion_sdk/portability\
 -Ifusion_sdk/gcast/src\
 -Ifusion_sdk/calvin_files/fusion/src\
 -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter\
 -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter\
 -D_USE_MEM_MAPPING_

SOURCES.fusion = \
	fusion_sdk/file/BARFileData.cpp\
	fusion_sdk/file/BPMAPFileData.cpp\
	fusion_sdk/file/CDFFileData.cpp\
	fusion_sdk/file/CELFileData.cpp\
	fusion_sdk/file/CHPFileData.cpp\
	fusion_sdk/file/EXPFileData.cpp\
	fusion_sdk/file/FileIO.cpp\
	fusion_sdk/file/GRCFileData.cpp\
	fusion_sdk/file/MSKFileData.cpp\
	fusion_sdk/file/PSIFileData.cpp\
	fusion_sdk/gcast/src/GridControlData.cpp\
	fusion_sdk/calvin_files/array/src/ArrayAttributes.cpp\
	fusion_sdk/calvin_files/array/src/ArrayAudit.cpp\
	fusion_sdk/calvin_files/array/src/ArrayData.cpp\
	fusion_sdk/calvin_files/data/src/CDFData.cpp\
	fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp\
	fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp\
	fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp\
	fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp\
	fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp\
	fusion_sdk/calvin_files/data/src/CELData.cpp\
	fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp\
	fusion_sdk/calvin_files/data/src/CHPData.cpp\
	fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp\
	fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp\
	fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp\
	fusion_sdk/calvin_files/data/src/DATData.cpp\
	fusion_sdk/calvin_files/data/src/DataGroup.cpp\
	fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp\
	fusion_sdk/calvin_files/data/src/DataSet.cpp\
	fusion_sdk/calvin_files/data/src/DataSetHeader.cpp\
	fusion_sdk/calvin_files/data/src/FileHeader.cpp\
	fusion_sdk/calvin_files/data/src/GenericData.cpp\
	fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp\
	fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.cpp\
	fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp\
	fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp\
	fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp\
	fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp\
	fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp\
	fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp\
	fusion_sdk/calvin_files/parsers/src/AuditFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/DATFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp\
	fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp\
	fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp\
	fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp\
	fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp\
	fusion_sdk/calvin_files/parsers/src/FileInput.cpp\
	fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp\
	fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/GridControlFileReader.cpp\
	fusion_sdk/calvin_files/parsers/src/TextFileReader.cpp\
	fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp\
	fusion_sdk/calvin_files/utils/src/DateTime.cpp\
	fusion_sdk/calvin_files/utils/src/FileUtils.cpp\
	fusion_sdk/calvin_files/utils/src/StringUtils.cpp\
	fusion_sdk/calvin_files/utils/src/checksum.cpp

SOURCES.package = \
	R_affx_cel_parser.cpp\
	R_affx_cdf_parser.cpp\
	R_affx_cdf_extras.cpp

OBJS=$(SOURCES.fusion:.cpp=.o) $(SOURCES.package:.cpp=.o)
 
## The files below are the ones left out of the 
##   makefile.mac from the fusion zip archive
##	fusion_sdk/file/DttArrayFileReader.cpp\
##	fusion_sdk/file/SAXDttArrayHandlers.cpp\
##	fusion_sdk/calvin_files/fusion/src/FusionArrayFileReader.cpp\
##	fusion_sdk/calvin_files/parsers/src/ArrayFileReader.cpp\
##	fusion_sdk/calvin_files/parsers/src/SAXArrayHandlers.cpp\
