AUTOMAKE_OPTIONS = subdir-objects
lib_LTLIBRARIES = libpwiz.la
LDADD = libpwiz.la $(LIBS)
ACLOCAL_AMFLAGS = -I .
LIBS = $(BOOST_THREAD_LIBS) $(BOOST_THREADS_LIBS) $(BOOST_FILESYSTEM_LIBS) $(BOOST_REGEX_LIBS) $(BOOST_SERIALIZATION_LIBS) $(BOOST_SYSTEM_LIBS) $(BOOST_IOSTREAMS_LIBS) $(BOOST_DATE_TIME_LIBS) $(BOOST_PROGRAM_OPTIONS_LIBS) $(BOOST_CHRONO_LIBS)
AM_LDFLAGS = -L$(BOOST_LDPATH) $(BOOST_THREADS_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_REGEX_LDFLAGS) $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_IOSTREAMS_LDFLAGS) $(BOOST_DATE_TIME_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_CHRONO_LDFLAGS)
AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I"libraries/boost_aux" -I"pwiz/data/msdata/ramp" -I"libraries/Eigen" -I"libraries/CSpline" -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSERTS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER
libpwiz_la_SOURCES =  ./libraries/boost_aux/libs/nowide/src/iostream.cpp ./pwiz/utility/math/erf.cpp ./pwiz/data/identdata/Version.cpp pwiz/data/tradata/Reader.cpp ./pwiz/data/msdata/Diff.cpp ./pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp ./pwiz/analysis/peakdetect/PeakFitter.cpp ./pwiz/data/vendor_readers/UNIFI/SpectrumList_UNIFI.cpp ./pwiz/utility/minimxml/XMLWriter.cpp pwiz/data/tradata/DefaultReaderList.cpp ./pwiz/analysis/demux/DemuxDebugWriter.cpp ./pwiz/data/msdata/BinaryDataEncoder.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_3D.cpp ./pwiz/analysis/passive/RegionSlice.cpp ./pwiz/analysis/peptideid/PeptideIDMap.cpp ./pwiz/analysis/frequency/TruncatedLorentzianEstimator.cpp ./pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefault.cpp ./pwiz/utility/proteome/IPIFASTADatabase.cpp pwiz/Version.cpp ./pwiz/data/vendor_readers/UNIFI/Reader_UNIFI_Detail.cpp ./pwiz/data/identdata/IdentData.cpp ./pwiz/data/msdata/Version.cpp ./pwiz/analysis/peakdetect/PeakelPicker.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.cpp ./pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.cpp ./pwiz/data/msdata/SpectrumListCache.cpp pwiz_tools/common/MSDataAnalyzerApplication.cpp ./pwiz/analysis/demux/CubicHermiteSpline.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.cpp ./pwiz/utility/misc/TabReader.cpp ./pwiz/analysis/peakdetect/FeatureModeler.cpp ./pwiz/data/msdata/Serializer_MSn.cpp ./pwiz/data/common/diff_std.cpp ./pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp ./pwiz/analysis/peakdetect/PeakelGrower.cpp ./pwiz/data/proteome/AminoAcid.cpp ./pwiz/data/proteome/DefaultReaderList.cpp ./pwiz/analysis/peptideid/PeptideID_pepXML.cpp ./pwiz/analysis/frequency/PeakDetectorMatchedFilterTestData.cpp ./pwiz/analysis/peakdetect/PeakExtractor.cpp ./pwiz/utility/misc/Base64.cpp ./pwiz/data/msdata/SpectrumList_BTDX.cpp ./pwiz/data/msdata/MSDataFile.cpp ./pwiz/data/proteome/Reader_FASTA.cpp ./pwiz/data/msdata/IO.cpp ./pwiz/analysis/common/CwtPeakDetector.cpp ./pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp ./pwiz/utility/misc/SHA1.cpp ./pwiz/utility/misc/VendorReaderTestHarness.cpp ./pwiz/analysis/demux/DemuxSolver.cpp ./pwiz/data/msdata/SpectrumWorkerThreads.cpp ./pwiz/data/identdata/DelimWriter.cpp pwiz/data/tradata/IO.cpp ./pwiz/analysis/frequency/TruncatedLorentzian.cpp pwiz/data/tradata/TraData.cpp ./pwiz/data/msdata/SpectrumList_MSn.cpp pwiz/analysis/proteome_processing/ProteinList_DecoyGenerator.cpp ./pwiz/analysis/demux/MatrixIO.cpp ./pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.cpp ./pwiz/analysis/common/WhittakerSmoother.cpp ./pwiz/analysis/demux/OverlapDemultiplexer.cpp ./pwiz/data/common/cv.cpp ./pwiz/analysis/demux/DemuxDebugReader.cpp ./pwiz/data/msdata/MSNumpress.cpp ./pwiz/data/msdata/examples.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_MZWindow.cpp ./pwiz/analysis/demux/PrecursorMaskCodec.cpp pwiz/data/tradata/Diff.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_Smoother.cpp ./pwiz/data/proteome/Digestion.cpp ./pwiz/data/vendor_readers/Bruker/Reader_Bruker.cpp ./pwiz/data/msdata/ChromatogramList_mzML.cpp ./pwiz/data/misc/MinimumPepXML.cpp ./pwiz/utility/chemistry/IsotopeEnvelopeEstimator.cpp ./pwiz/analysis/common/SavitzkyGolaySmoother.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculator.cpp pwiz/analysis/proteome_processing/ProteinListFactory.cpp ./pwiz/utility/math/Stats.cpp ./pwiz/analysis/passive/RegionAnalyzer.cpp ./pwiz/data/identdata/Serializer_Text.cpp ./pwiz/analysis/passive/RegionTIC.cpp ./pwiz/data/proteome/Serializer_FASTA.cpp ./pwiz/data/proteome/Modification.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp ./pwiz/analysis/spectrum_processing/ThresholdFilter.cpp ./pwiz/data/misc/FrequencyDataTestData.cpp ./pwiz/data/msdata/SpectrumList_MGF.cpp ./pwiz/data/vendor_readers/Thermo/ChromatogramList_Thermo.cpp ./pwiz/data/identdata/Serializer_pepXML.cpp ./pwiz/analysis/peakdetect/MZRTField.cpp ./pwiz/data/proteome/Diff.cpp ./pwiz/utility/chemistry/Chemistry.cpp ./pwiz/data/identdata/Diff.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_Filter.cpp ./pwiz/data/proteome/ProteinListCache.cpp ./pwiz/analysis/peakdetect/Noise.cpp pwiz/data/tradata/Version.cpp ./pwiz/utility/chemistry/ChemistryData.cpp ./libraries/CSpline/CSpline.cpp ./pwiz/data/msdata/Index_mzML.cpp ./pwiz/analysis/frequency/ParameterEstimator.cpp ./pwiz/analysis/frequency/FrequencyEstimatorSimple.cpp ./pwiz/analysis/chromatogram_processing/ChromatogramList_Filter.cpp ./pwiz/analysis/passive/PepXMLCat.cpp ./pwiz/analysis/peakdetect/FeatureDetectorPeakel.cpp ./pwiz/analysis/spectrum_processing/MS2Deisotoper.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.cpp ./pwiz/data/vendor_readers/Waters/Reader_Waters.cpp ./pwiz/data/msdata/SpectrumInfo.cpp ./pwiz/analysis/peptideid/PeptideID_flat.cpp ./pwiz/data/identdata/examples.cpp ./pwiz/analysis/frequency/FrequencyEstimatorPhysicalModel.cpp ./pwiz/utility/misc/IntegerSet.cpp ./pwiz/analysis/chromatogram_processing/ChromatogramList_SavitzkyGolaySmoother.cpp ./pwiz/analysis/demux/MSXDemultiplexer.cpp ./pwiz/analysis/Version.cpp ./pwiz/data/common/MemoryIndex.cpp ./pwiz/analysis/spectrum_processing/PrecursorMassFilter.cpp ./pwiz/data/vendor_readers/Thermo/Reader_Thermo.cpp ./pwiz/utility/misc/SHA1Calculator.cpp ./pwiz/analysis/peakdetect/PeakFamilyDetector.cpp ./pwiz/analysis/peakdetect/PeakFamilyDetectorFTTestData.cpp ./pwiz/data/identdata/DelimReader.cpp ./pwiz/data/msdata/References.cpp ./pwiz/analysis/passive/MetadataReporter.cpp ./pwiz/analysis/spectrum_processing/SpectrumListFactory.cpp pwiz/analysis/proteome_processing/ProteinList_Filter.cpp ./pwiz/data/vendor_readers/ABI/SpectrumList_ABI.cpp ./pwiz/analysis/passive/MSDataCache.cpp ./pwiz/analysis/passive/SpectrumTable.cpp ./pwiz/data/vendor_readers/UIMF/Reader_UIMF.cpp ./pwiz/analysis/peakdetect/PeakFinder.cpp ./pwiz/data/proteome/examples.cpp ./pwiz/data/msdata/MSData.cpp ./pwiz/utility/chemistry/IsotopeCalculator.cpp ./pwiz/data/vendor_readers/ExtendedReaderList.cpp ./pwiz/analysis/frequency/PeakDetectorNaive.cpp ./pwiz/data/proteome/Reader.cpp ./pwiz/data/misc/FrequencyData.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_ZeroSamplesFilter.cpp ./pwiz/utility/misc/BinaryData.cpp ./pwiz/data/identdata/Serializer_protXML.cpp ./pwiz/utility/chemistry/MZTolerance.cpp ./pwiz/data/vendor_readers/UNIFI/Reader_UNIFI.cpp ./pwiz/data/vendor_readers/Agilent/ChromatogramList_Agilent.cpp ./pwiz/analysis/spectrum_processing/MS2NoiseFilter.cpp ./pwiz/data/identdata/Reader.cpp ./pwiz/utility/misc/IterationListener.cpp pwiz/data/tradata/examples.cpp ./pwiz/data/common/CVTranslator.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.cpp ./pwiz/data/common/Unimod.cpp ./pwiz/data/proteome/Version.cpp ./pwiz/data/identdata/IO.cpp ./pwiz/data/msdata/Serializer_mzXML.cpp ./pwiz/data/identdata/DefaultReaderList.cpp ./pwiz/analysis/frequency/PeakDetectorMatchedFilter.cpp ./pwiz/analysis/common/ExtraZeroSamplesFilter.cpp ./pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.cpp ./pwiz/utility/minimxml/SAXParser.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.cpp ./pwiz/data/identdata/IdentDataFile.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_Demux.cpp ./pwiz/data/msdata/Serializer_mzML.cpp ./pwiz/data/identdata/Pep2MzIdent.cpp ./pwiz/data/vendor_readers/Shimadzu/Reader_Shimadzu.cpp ./pwiz/analysis/passive/RegionSIC.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.cpp ./pwiz/analysis/passive/RunSummary.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.cpp pwiz/data/tradata/References.cpp ./pwiz/data/vendor_readers/Shimadzu/ChromatogramList_Shimadzu.cpp ./pwiz/analysis/common/ZeroSampleFiller.cpp ./pwiz/utility/misc/MSIHandler.cpp ./pwiz/data/msdata/LegacyAdapter.cpp ./pwiz/data/msdata/MSDataMerger.cpp ./pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.cpp ./pwiz/data/proteome/ProteomeData.cpp ./pwiz/analysis/common/LocalMaximumPeakDetector.cpp ./pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.cpp ./pwiz/analysis/passive/MSDataAnalyzer.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_MZRefiner.cpp ./pwiz/analysis/chromatogram_processing/ChromatogramList_XICGenerator.cpp ./pwiz/utility/math/Parabola.cpp ./pwiz/data/msdata/Serializer_MGF.cpp ./pwiz/data/vendor_readers/Bruker/ChromatogramList_Bruker.cpp ./pwiz/data/vendor_readers/ABI/Reader_ABI.cpp ./pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp ./pwiz/data/common/BinaryIndexStream.cpp ./pwiz/analysis/passive/SpectrumBinaryData.cpp ./pwiz/data/common/obo.cpp ./pwiz/data/vendor_readers/UIMF/SpectrumList_UIMF.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotope.cpp ./pwiz/utility/chemistry/IsotopeTable.cpp ./pwiz/analysis/demux/DemuxHelpers.cpp ./libraries/libsvm-3.0/svm.cpp ./pwiz/analysis/demux/SpectrumPeakExtractor.cpp ./pwiz/data/msdata/SpectrumList_mzXML.cpp ./pwiz/data/common/ParamTypes.cpp pwiz/data/tradata/Serializer_traML.cpp ./pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp ./pwiz/data/msdata/DefaultReaderList.cpp ./pwiz/data/misc/PeakData.cpp ./pwiz/analysis/passive/TabularConfig.cpp ./pwiz/data/vendor_readers/Waters/SpectrumList_Waters.cpp ./pwiz/analysis/chromatogram_processing/ChromatogramListFactory.cpp ./pwiz/analysis/frequency/MagnitudeLorentzian.cpp ./pwiz/data/proteome/Peptide.cpp ./pwiz/data/msdata/SpectrumList_mzML.cpp ./pwiz/data/vendor_readers/Shimadzu/SpectrumList_Shimadzu.cpp ./pwiz/data/msdata/Reader.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_Sorter.cpp ./pwiz/utility/misc/Filesystem.cpp ./pwiz/analysis/spectrum_processing/SpectrumList_PeakFilter.cpp ./pwiz/analysis/frequency/TruncatedLorentzianParameters.cpp ./pwiz/utility/misc/random_access_compressed_ifstream.cpp ./pwiz/analysis/chromatogram_processing/ChromatogramList_LockmassRefiner.cpp ./pwiz/data/vendor_readers/Agilent/Reader_Agilent.cpp pwiz/data/tradata/TraDataFile.cpp ./pwiz/data/proteome/ProteomeDataFile.cpp ./pwiz/data/identdata/KwCVMap.cpp ./pwiz/data/identdata/Serializer_mzid.cpp ./pwiz/data/identdata/References.cpp ./pwiz/analysis/frequency/MagnitudeLorentzianTestData.cpp ./pwiz/data/msdata/SpectrumIterator.cpp
libpwiz_la_LDFLAGS = -L$(BOOST_LDPATH) -version-info 3:0:0
#
# here are some programs that test the pwiz library.
#
check_PROGRAMS = filter_gaussfiltertest msdata_Serializer_MSn_Test ABI_Reader_ABI_Test proteome_processing_ProteinList_FilterTest msdata_MSDataTest Bruker_Reader_Bruker_Test misc_MinimumPepXMLTest peakdetect_MZRTFieldTest msdata_MSDataMergerTest math_StatsTest proteome_PeptideTest math_qrTest msdata_ReaderTest peakdetect_NoiseTest frequency_PeakDetectorMatchedFilterTest msdata_BinaryDataEncoderTest misc_IntegerSetTest misc_Base64Test spectrum_processing_SpectrumList_FilterTest math_LinearSolverTest math_erfTest proteome_ReaderTest peptideid_PeptideIDMapTest proteome_ProteomeDataFileTest spectrum_processing_SpectrumList_PrecursorRecalculatorTest msdata_SpectrumInfoTest spectrum_processing_SpectrumList_PrecursorRefineTest math_MatchedFilterTest spectrum_processing_SpectrumList_DemuxTest math_LinearLeastSquaresTest chemistry_ChemistryTest identdata_Serializer_mzid_Test msdata_ChromatogramList_mzML_Test peakdetect_PeakFamilyDetectorFTTest spectrum_processing_SpectrumList_ChargeStateCalculatorTest peakdetect_FeatureDetectorPeakelTest spectrum_processing_MS2DeisotoperTest proteome_Serializer_FASTA_Test math_ParabolaTest msdata_SpectrumIteratorTest msdata_IOTest common_ExtraZeroSamplesFilterTest misc_FilesystemTest passive_MSDataAnalyzerTest common_SavitzkyGolaySmootherTest common_ZeroSampleFillerTest Agilent_Reader_Agilent_Test spectrum_processing_SpectrumList_ChargeFromIsotopeTest common_obotest msdata_Serializer_mzML_Test peakdetect_PeakFinderTest demux_CubicHermiteSplineTest minimxml_XMLWriterTest msdata_SpectrumList_mzML_Test proteome_processing_ProteinListFactoryTest misc_CalibrationParametersTest misc_PeakDataTest msdata_SpectrumList_mzXML_Test identdata_KwCVMapTest chemistry_IsotopeEnvelopeEstimatorTest common_ParamTypesTest peakdetect_FeatureModelerTest minimxml_SAXParserTest frequency_PeakDetectorNaiveTest Thermo_Reader_Thermo_Test math_OrderedPairTest misc_FrequencyDataTest misc_SampleDatumTest filter_filterutilstest msdata_MSDataFileTest identdata_Serializer_pepXML_Test peakdetect_PeakelPickerTest spectrum_processing_SpectrumList_SorterTest msdata_LegacyAdapterTest frequency_MagnitudeLorentzianTest demux_SpectrumPeakExtractorTest identdata_IdentDataTest common_CwtPeakDetectorTest demux_DemuxHelpersTest msdata_Serializer_MGF_Test identdata_Serializer_Text_Test misc_SHA1_ostream_test demux_MatrixIOTest resample_convert2densetest common_CVTranslatorTest peptideid_PeptideID_flatTest proteome_DiffTest chemistry_MZToleranceTest common_WhittakerSmootherTest spectrum_processing_SpectrumListFactoryTest spectrum_processing_SpectrumList_ScanSummerTest proteome_IPIFASTADatabaseTest misc_ExceptionTest spectrum_processing_SpectrumList_PeakFilterTest base_copy_iftest common_MSDataAnalyzerApplicationTest proteome_AminoAcidTest peakdetect_PeakFitterTest common_LocalMaximumPeakDetectorTest spectrum_processing_SpectrumList_MZWindowTest chemistry_IsotopeCalculatorTest peakdetect_PeakelGrowerTest misc_BinaryDataTest misc_endian_test peakdetect_FeatureDetectorTuningTest spectrum_processing_SpectrumList_MZRefinerTest msdata_ReferencesTest misc_IterationListenerTest common_MemoryIndexTest proteome_ProteinListWrapperTest peptideid_PeptideID_pepXMLTest misc_TabReaderTest misc_mru_list_test frequency_TruncatedLorentzianParametersTest resample_determinbinwithtest demux_DemuxDebugReadWriteTest msdata_SpectrumList_MGF_Test identdata_DiffTest frequency_TruncatedLorentzianTest identdata_Serializer_protXML_Test msdata_SpectrumListBaseTest msdata_MSnReaderTest chemistry_IsotopeTableTest resample_bucket1dtest frequency_FrequencyEstimatorSimpleTest spectrum_processing_PrecursorRecalculatorDefaultTest msdata_SpectrumListWrapperTest misc_almost_equal_test base_cumsumtest ms_simplepickertest proteome_ProteomeDataTest proteome_processing_ProteinList_DecoyGeneratorTest misc_SHA1CalculatorTest common_cvtest msdata_DiffTest base_basetest proteome_DigestionTest peakdetect_FeatureDetectorSimpleTest msdata_Serializer_mzXML_Test identdata_ReferencesTest demux_DemuxSolverTest frequency_FrequencyEstimatorPhysicalModelTest base_equispaceinterpolationtest proteome_ProteinListCacheTest misc_DateTimeTest peakdetect_PeakExtractorTest common_UnimodTest msdata_ChromatogramListBaseTest identdata_IOTest spectrum_processing_SpectrumList_MetadataFixerTest passive_MSDataCacheTest msdata_SpectrumListCacheTest common_BinaryIndexStreamTest common_diff_std_test msdata_SpectrumList_MSn_Test
filter_gaussfiltertest_SOURCES=./pwiz/utility/findmf/base/filter/gaussfiltertest.cpp
msdata_Serializer_MSn_Test_SOURCES=./pwiz/data/msdata/Serializer_MSn_Test.cpp
ABI_Reader_ABI_Test_SOURCES=./pwiz/data/vendor_readers/ABI/Reader_ABI_Test.cpp
proteome_processing_ProteinList_FilterTest_SOURCES=pwiz/analysis/proteome_processing/ProteinList_FilterTest.cpp
msdata_MSDataTest_SOURCES=./pwiz/data/msdata/MSDataTest.cpp
Bruker_Reader_Bruker_Test_SOURCES=./pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.cpp
misc_MinimumPepXMLTest_SOURCES=./pwiz/data/misc/MinimumPepXMLTest.cpp
peakdetect_MZRTFieldTest_SOURCES=./pwiz/analysis/peakdetect/MZRTFieldTest.cpp
msdata_MSDataMergerTest_SOURCES=./pwiz/data/msdata/MSDataMergerTest.cpp
math_StatsTest_SOURCES=./pwiz/utility/math/StatsTest.cpp
proteome_PeptideTest_SOURCES=./pwiz/data/proteome/PeptideTest.cpp
math_qrTest_SOURCES=./pwiz/utility/math/qrTest.cpp
msdata_ReaderTest_SOURCES=./pwiz/data/msdata/ReaderTest.cpp
peakdetect_NoiseTest_SOURCES=./pwiz/analysis/peakdetect/NoiseTest.cpp
frequency_PeakDetectorMatchedFilterTest_SOURCES=./pwiz/analysis/frequency/PeakDetectorMatchedFilterTest.cpp
msdata_BinaryDataEncoderTest_SOURCES=./pwiz/data/msdata/BinaryDataEncoderTest.cpp
misc_IntegerSetTest_SOURCES=./pwiz/utility/misc/IntegerSetTest.cpp
misc_Base64Test_SOURCES=./pwiz/utility/misc/Base64Test.cpp
spectrum_processing_SpectrumList_FilterTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp
math_LinearSolverTest_SOURCES=./pwiz/utility/math/LinearSolverTest.cpp
math_erfTest_SOURCES=./pwiz/utility/math/erfTest.cpp
proteome_ReaderTest_SOURCES=./pwiz/data/proteome/ReaderTest.cpp
peptideid_PeptideIDMapTest_SOURCES=./pwiz/analysis/peptideid/PeptideIDMapTest.cpp
proteome_ProteomeDataFileTest_SOURCES=./pwiz/data/proteome/ProteomeDataFileTest.cpp
spectrum_processing_SpectrumList_PrecursorRecalculatorTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp
msdata_SpectrumInfoTest_SOURCES=./pwiz/data/msdata/SpectrumInfoTest.cpp
spectrum_processing_SpectrumList_PrecursorRefineTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefineTest.cpp
math_MatchedFilterTest_SOURCES=./pwiz/utility/math/MatchedFilterTest.cpp
spectrum_processing_SpectrumList_DemuxTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_DemuxTest.cpp
math_LinearLeastSquaresTest_SOURCES=./pwiz/utility/math/LinearLeastSquaresTest.cpp
chemistry_ChemistryTest_SOURCES=./pwiz/utility/chemistry/ChemistryTest.cpp
identdata_Serializer_mzid_Test_SOURCES=./pwiz/data/identdata/Serializer_mzid_Test.cpp
msdata_ChromatogramList_mzML_Test_SOURCES=./pwiz/data/msdata/ChromatogramList_mzML_Test.cpp
peakdetect_PeakFamilyDetectorFTTest_SOURCES=./pwiz/analysis/peakdetect/PeakFamilyDetectorFTTest.cpp
spectrum_processing_SpectrumList_ChargeStateCalculatorTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculatorTest.cpp
peakdetect_FeatureDetectorPeakelTest_SOURCES=./pwiz/analysis/peakdetect/FeatureDetectorPeakelTest.cpp
spectrum_processing_MS2DeisotoperTest_SOURCES=./pwiz/analysis/spectrum_processing/MS2DeisotoperTest.cpp
proteome_Serializer_FASTA_Test_SOURCES=./pwiz/data/proteome/Serializer_FASTA_Test.cpp
math_ParabolaTest_SOURCES=./pwiz/utility/math/ParabolaTest.cpp
msdata_SpectrumIteratorTest_SOURCES=./pwiz/data/msdata/SpectrumIteratorTest.cpp
msdata_IOTest_SOURCES=./pwiz/data/msdata/IOTest.cpp
common_ExtraZeroSamplesFilterTest_SOURCES=./pwiz/analysis/common/ExtraZeroSamplesFilterTest.cpp
misc_FilesystemTest_SOURCES=./pwiz/utility/misc/FilesystemTest.cpp
passive_MSDataAnalyzerTest_SOURCES=./pwiz/analysis/passive/MSDataAnalyzerTest.cpp
common_SavitzkyGolaySmootherTest_SOURCES=./pwiz/analysis/common/SavitzkyGolaySmootherTest.cpp
common_ZeroSampleFillerTest_SOURCES=./pwiz/analysis/common/ZeroSampleFillerTest.cpp
Agilent_Reader_Agilent_Test_SOURCES=./pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.cpp
spectrum_processing_SpectrumList_ChargeFromIsotopeTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotopeTest.cpp
common_obotest_SOURCES=./pwiz/data/common/obotest.cpp
msdata_Serializer_mzML_Test_SOURCES=./pwiz/data/msdata/Serializer_mzML_Test.cpp
peakdetect_PeakFinderTest_SOURCES=./pwiz/analysis/peakdetect/PeakFinderTest.cpp
demux_CubicHermiteSplineTest_SOURCES=./pwiz/analysis/demux/CubicHermiteSplineTest.cpp
minimxml_XMLWriterTest_SOURCES=./pwiz/utility/minimxml/XMLWriterTest.cpp
msdata_SpectrumList_mzML_Test_SOURCES=./pwiz/data/msdata/SpectrumList_mzML_Test.cpp
proteome_processing_ProteinListFactoryTest_SOURCES=pwiz/analysis/proteome_processing/ProteinListFactoryTest.cpp
misc_CalibrationParametersTest_SOURCES=./pwiz/data/misc/CalibrationParametersTest.cpp
misc_PeakDataTest_SOURCES=./pwiz/data/misc/PeakDataTest.cpp
msdata_SpectrumList_mzXML_Test_SOURCES=./pwiz/data/msdata/SpectrumList_mzXML_Test.cpp
identdata_KwCVMapTest_SOURCES=./pwiz/data/identdata/KwCVMapTest.cpp
chemistry_IsotopeEnvelopeEstimatorTest_SOURCES=./pwiz/utility/chemistry/IsotopeEnvelopeEstimatorTest.cpp
common_ParamTypesTest_SOURCES=./pwiz/data/common/ParamTypesTest.cpp
peakdetect_FeatureModelerTest_SOURCES=./pwiz/analysis/peakdetect/FeatureModelerTest.cpp
minimxml_SAXParserTest_SOURCES=./pwiz/utility/minimxml/SAXParserTest.cpp
frequency_PeakDetectorNaiveTest_SOURCES=./pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp
Thermo_Reader_Thermo_Test_SOURCES=./pwiz/data/vendor_readers/Thermo/Reader_Thermo_Test.cpp
math_OrderedPairTest_SOURCES=./pwiz/utility/math/OrderedPairTest.cpp
misc_FrequencyDataTest_SOURCES=./pwiz/data/misc/FrequencyDataTest.cpp
misc_SampleDatumTest_SOURCES=./pwiz/data/misc/SampleDatumTest.cpp
filter_filterutilstest_SOURCES=./pwiz/utility/findmf/base/filter/filterutilstest.cpp
msdata_MSDataFileTest_SOURCES=./pwiz/data/msdata/MSDataFileTest.cpp
identdata_Serializer_pepXML_Test_SOURCES=./pwiz/data/identdata/Serializer_pepXML_Test.cpp
peakdetect_PeakelPickerTest_SOURCES=./pwiz/analysis/peakdetect/PeakelPickerTest.cpp
spectrum_processing_SpectrumList_SorterTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp
msdata_LegacyAdapterTest_SOURCES=./pwiz/data/msdata/LegacyAdapterTest.cpp
frequency_MagnitudeLorentzianTest_SOURCES=./pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp
demux_SpectrumPeakExtractorTest_SOURCES=./pwiz/analysis/demux/SpectrumPeakExtractorTest.cpp
identdata_IdentDataTest_SOURCES=./pwiz/data/identdata/IdentDataTest.cpp
common_CwtPeakDetectorTest_SOURCES=./pwiz/analysis/common/CwtPeakDetectorTest.cpp
demux_DemuxHelpersTest_SOURCES=./pwiz/analysis/demux/DemuxHelpersTest.cpp
msdata_Serializer_MGF_Test_SOURCES=./pwiz/data/msdata/Serializer_MGF_Test.cpp
identdata_Serializer_Text_Test_SOURCES=./pwiz/data/identdata/Serializer_Text_Test.cpp
misc_SHA1_ostream_test_SOURCES=./pwiz/utility/misc/SHA1_ostream_test.cpp
demux_MatrixIOTest_SOURCES=./pwiz/analysis/demux/MatrixIOTest.cpp
resample_convert2densetest_SOURCES=./pwiz/utility/findmf/base/resample/convert2densetest.cpp
common_CVTranslatorTest_SOURCES=./pwiz/data/common/CVTranslatorTest.cpp
peptideid_PeptideID_flatTest_SOURCES=./pwiz/analysis/peptideid/PeptideID_flatTest.cpp
proteome_DiffTest_SOURCES=./pwiz/data/proteome/DiffTest.cpp
chemistry_MZToleranceTest_SOURCES=./pwiz/utility/chemistry/MZToleranceTest.cpp
common_WhittakerSmootherTest_SOURCES=./pwiz/analysis/common/WhittakerSmootherTest.cpp
spectrum_processing_SpectrumListFactoryTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp
spectrum_processing_SpectrumList_ScanSummerTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_ScanSummerTest.cpp
proteome_IPIFASTADatabaseTest_SOURCES=./pwiz/utility/proteome/IPIFASTADatabaseTest.cpp
misc_ExceptionTest_SOURCES=./pwiz/utility/misc/ExceptionTest.cpp
spectrum_processing_SpectrumList_PeakFilterTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_PeakFilterTest.cpp
base_copy_iftest_SOURCES=./pwiz/utility/findmf/base/base/copy_iftest.cpp
common_MSDataAnalyzerApplicationTest_SOURCES=pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp
proteome_AminoAcidTest_SOURCES=./pwiz/data/proteome/AminoAcidTest.cpp
peakdetect_PeakFitterTest_SOURCES=./pwiz/analysis/peakdetect/PeakFitterTest.cpp
common_LocalMaximumPeakDetectorTest_SOURCES=./pwiz/analysis/common/LocalMaximumPeakDetectorTest.cpp
spectrum_processing_SpectrumList_MZWindowTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_MZWindowTest.cpp
chemistry_IsotopeCalculatorTest_SOURCES=./pwiz/utility/chemistry/IsotopeCalculatorTest.cpp
peakdetect_PeakelGrowerTest_SOURCES=./pwiz/analysis/peakdetect/PeakelGrowerTest.cpp
misc_BinaryDataTest_SOURCES=./pwiz/utility/misc/BinaryDataTest.cpp
misc_endian_test_SOURCES=./pwiz/utility/misc/endian_test.cpp
peakdetect_FeatureDetectorTuningTest_SOURCES=./pwiz/analysis/peakdetect/FeatureDetectorTuningTest.cpp
spectrum_processing_SpectrumList_MZRefinerTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_MZRefinerTest.cpp
msdata_ReferencesTest_SOURCES=./pwiz/data/msdata/ReferencesTest.cpp
misc_IterationListenerTest_SOURCES=./pwiz/utility/misc/IterationListenerTest.cpp
common_MemoryIndexTest_SOURCES=./pwiz/data/common/MemoryIndexTest.cpp
proteome_ProteinListWrapperTest_SOURCES=./pwiz/data/proteome/ProteinListWrapperTest.cpp
peptideid_PeptideID_pepXMLTest_SOURCES=./pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp
misc_TabReaderTest_SOURCES=./pwiz/utility/misc/TabReaderTest.cpp
misc_mru_list_test_SOURCES=./pwiz/utility/misc/mru_list_test.cpp
frequency_TruncatedLorentzianParametersTest_SOURCES=./pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp
resample_determinbinwithtest_SOURCES=./pwiz/utility/findmf/base/resample/determinbinwithtest.cpp
demux_DemuxDebugReadWriteTest_SOURCES=./pwiz/analysis/demux/DemuxDebugReadWriteTest.cpp
msdata_SpectrumList_MGF_Test_SOURCES=./pwiz/data/msdata/SpectrumList_MGF_Test.cpp
identdata_DiffTest_SOURCES=./pwiz/data/identdata/DiffTest.cpp
frequency_TruncatedLorentzianTest_SOURCES=./pwiz/analysis/frequency/TruncatedLorentzianTest.cpp
identdata_Serializer_protXML_Test_SOURCES=./pwiz/data/identdata/Serializer_protXML_Test.cpp
msdata_SpectrumListBaseTest_SOURCES=./pwiz/data/msdata/SpectrumListBaseTest.cpp
msdata_MSnReaderTest_SOURCES=./pwiz/data/msdata/MSnReaderTest.cpp
chemistry_IsotopeTableTest_SOURCES=./pwiz/utility/chemistry/IsotopeTableTest.cpp
resample_bucket1dtest_SOURCES=./pwiz/utility/findmf/base/resample/bucket1dtest.cpp
frequency_FrequencyEstimatorSimpleTest_SOURCES=./pwiz/analysis/frequency/FrequencyEstimatorSimpleTest.cpp
spectrum_processing_PrecursorRecalculatorDefaultTest_SOURCES=./pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefaultTest.cpp
msdata_SpectrumListWrapperTest_SOURCES=./pwiz/data/msdata/SpectrumListWrapperTest.cpp
misc_almost_equal_test_SOURCES=./pwiz/utility/misc/almost_equal_test.cpp
base_cumsumtest_SOURCES=./pwiz/utility/findmf/base/base/cumsumtest.cpp
ms_simplepickertest_SOURCES=./pwiz/utility/findmf/base/ms/simplepickertest.cpp
proteome_ProteomeDataTest_SOURCES=./pwiz/data/proteome/ProteomeDataTest.cpp
proteome_processing_ProteinList_DecoyGeneratorTest_SOURCES=pwiz/analysis/proteome_processing/ProteinList_DecoyGeneratorTest.cpp
misc_SHA1CalculatorTest_SOURCES=./pwiz/utility/misc/SHA1CalculatorTest.cpp
common_cvtest_SOURCES=./pwiz/data/common/cvtest.cpp
msdata_DiffTest_SOURCES=./pwiz/data/msdata/DiffTest.cpp
base_basetest_SOURCES=./pwiz/utility/findmf/base/base/basetest.cpp
proteome_DigestionTest_SOURCES=./pwiz/data/proteome/DigestionTest.cpp
peakdetect_FeatureDetectorSimpleTest_SOURCES=./pwiz/analysis/peakdetect/FeatureDetectorSimpleTest.cpp
msdata_Serializer_mzXML_Test_SOURCES=./pwiz/data/msdata/Serializer_mzXML_Test.cpp
identdata_ReferencesTest_SOURCES=./pwiz/data/identdata/ReferencesTest.cpp
demux_DemuxSolverTest_SOURCES=./pwiz/analysis/demux/DemuxSolverTest.cpp
frequency_FrequencyEstimatorPhysicalModelTest_SOURCES=./pwiz/analysis/frequency/FrequencyEstimatorPhysicalModelTest.cpp
base_equispaceinterpolationtest_SOURCES=./pwiz/utility/findmf/base/base/equispaceinterpolationtest.cpp
proteome_ProteinListCacheTest_SOURCES=./pwiz/data/proteome/ProteinListCacheTest.cpp
misc_DateTimeTest_SOURCES=./pwiz/utility/misc/DateTimeTest.cpp
peakdetect_PeakExtractorTest_SOURCES=./pwiz/analysis/peakdetect/PeakExtractorTest.cpp
common_UnimodTest_SOURCES=./pwiz/data/common/UnimodTest.cpp
msdata_ChromatogramListBaseTest_SOURCES=./pwiz/data/msdata/ChromatogramListBaseTest.cpp
identdata_IOTest_SOURCES=./pwiz/data/identdata/IOTest.cpp
spectrum_processing_SpectrumList_MetadataFixerTest_SOURCES=./pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixerTest.cpp
passive_MSDataCacheTest_SOURCES=./pwiz/analysis/passive/MSDataCacheTest.cpp
msdata_SpectrumListCacheTest_SOURCES=./pwiz/data/msdata/SpectrumListCacheTest.cpp
common_BinaryIndexStreamTest_SOURCES=./pwiz/data/common/BinaryIndexStreamTest.cpp
common_diff_std_test_SOURCES=./pwiz/data/common/diff_std_test.cpp
msdata_SpectrumList_MSn_Test_SOURCES=./pwiz/data/msdata/SpectrumList_MSn_Test.cpp
#
# here are some examples of programs that use the pwiz library.
#
bin_PROGRAMS = txt2mzml msconvert mscat hello_analyzer_2 idconvert write_example_files hello_msdata write_mzid_example_files hello_analyzer write_proteome_example_files pepcat write_traml_example_files
txt2mzml_SOURCES=./pwiz_tools/examples/txt2mzml.cpp
msconvert_SOURCES=pwiz_tools/commandline/msconvert.cpp
mscat_SOURCES=./pwiz_tools/examples/mscat.cpp
hello_analyzer_2_SOURCES=./pwiz_tools/examples/hello_analyzer_2.cpp
idconvert_SOURCES=pwiz_tools/commandline/idconvert.cpp
write_example_files_SOURCES=./pwiz_tools/examples/write_example_files.cpp
hello_msdata_SOURCES=./pwiz_tools/examples/hello_msdata.cpp
write_mzid_example_files_SOURCES=./pwiz_tools/examples/write_mzid_example_files.cpp
hello_analyzer_SOURCES=./pwiz_tools/examples/hello_analyzer.cpp
write_proteome_example_files_SOURCES=./pwiz_tools/examples/write_proteome_example_files.cpp
pepcat_SOURCES=pwiz_tools/commandline/pepcat.cpp
write_traml_example_files_SOURCES=./pwiz_tools/examples/write_traml_example_files.cpp