add_definitions("-g -O3")
add_library(all_lib
src/Common/auxfun.cpp          
src/MsCluster/MsClusterAuxfuns.cpp     
src/PepNovo/FastaDB.cpp      
src/PepNovo/EdgeModel.cpp      
src/PepNovo/PMC_rank.cpp
src/Common/BufferedOutputFile.cpp     
src/MsCluster/MsClusterBenchmark.cpp     
src/PepNovo/Fragmentation.cpp    
src/PepNovo/PmcsqsAdditionalFunctions.cpp
src/MLlib/mlauxfun.cpp          
src/MsCluster/MsClusterDataStorage.cpp     
src/PepNovo/FragmentSelection.cpp    
src/PepNovo/PMCSQS.cpp
src/MLlib/mlcgme.cpp          
src/PepNovo/FragProbTable.cpp    
src/PepNovo/PMCSQS_model.cpp
src/MLlib/mldataset.cpp         
src/MsCluster/MsParameterStruct.cpp    
src/PepNovo/Isotopes.cpp     
src/PepNovo/PMCSQSRanking.cpp
src/MLlib/mlfeature.cpp         
src/MsCluster/MsSimilarityModel.cpp    
src/PepNovo/MassRangeMap.cpp     
src/PepNovo/PrmGraph.cpp
src/MLlib/mllib.cpp         
src/PepNovo/AdvancedScoreModel.cpp     
src/PepNovo/ME_REG.cpp     
src/PepNovo/PrmNodeScoreModel.cpp
src/MLlib/mllogistic.cpp        
src/PepNovo/AdvancedScoreModel_regional.cpp  
src/PepNovo/ME_Regression_DataSet.cpp  
src/PepNovo/PTM_stuff.cpp
src/MLlib/mlmaximumentropy.cpp        
src/PepNovo/AllScoreModels.cpp       
src/PepNovo/ME_Regression_Model.cpp    
src/PepNovo/RankBoost.cpp
src/MLlib/mlmodel.cpp         
src/PepNovo/AllSpectraHolder.cpp       
src/PepNovo/MetaList.cpp     
src/PepNovo/RankBoostSample.cpp
src/MLlib/mloperatorlist.cpp        
src/PepNovo/AminoAcidProbs.cpp       
src/PepNovo/MultiPath.cpp      
src/PepNovo/RegionalPepNovoModel.cpp
src/MLlib/mloperatorsearch.cpp        
src/PepNovo/AnnotatedSpecturm.cpp      
#src/PepNovo/AnnotatedSpectrum.cpp      
src/PepNovo/AnnotatedSpectrum_add.cpp      
src/PepNovo/PartitionModel.cpp   
src/PepNovo/RegionalPrmNodeScoreModel.cpp
src/MLlib/MlRankBoostDataSet.cpp      
src/PepNovo/AnnotationFile.cpp       
src/PepNovo/PeakList.cpp     
src/PepNovo/RegularFragmentModel.cpp
src/MLlib/MlRankBoostModel.cpp        
src/PepNovo/base64.cpp         
src/PepNovo/PeakRank_advanced.cpp    
src/PepNovo/ReScoreDB.cpp
src/MLlib/mlscoremodel.cpp        
src/PepNovo/BasicDataStructs.cpp       
src/PepNovo/BasicDataStructs_add.cpp       
src/PepNovo/PeakRank_combined.cpp    
src/PepNovo/ScanList.cpp
src/MLlib/mltrainingcontainer.cpp     
src/PepNovo/Config.cpp         
src/PepNovo/PeakRank_combined_dnv.cpp  
src/PepNovo/SingleSpectrumHeader.cpp
src/MsCluster/Cluster.cpp       
src/PepNovo/ConversionTables.cpp       
src/PepNovo/PeakRankModel.cpp    
src/PepNovo/SpectraAggregator.cpp
src/MsCluster/ClusterOutputter.cpp    
src/PepNovo/CumulativeSeqProb.cpp      
src/PepNovo/PeakRankPartialDenovo.cpp  
src/PepNovo/SpectraFile.cpp
src/MsCluster/ClustFile.cpp       
src/PepNovo/DatFile.cpp        
src/PepNovo/PeakRank_simple.cpp    
src/PepNovo/SpectraList.cpp
src/MsCluster/DatFileManager.cpp      
src/PepNovo/DbFile.cpp         
src/PepNovo/PeakRankStats.cpp    
src/PepNovo/Spectrum.cpp
src/MsCluster/DatFileWriter.cpp       
src/PepNovo/DeNovoDp.cpp         
src/PepNovo/PepNovo_auxfun.cpp   
src/PepNovo/StrongFragmentModel.cpp
src/MsCluster/MsArchive.cpp       
src/PepNovo/DeNovoPartModel.cpp      
src/MsCluster/MsArchiveUpdater.cpp    
src/PepNovo/DeNovoRankTrain.cpp      
src/PepNovo/PeptideComp.cpp
src/MsCluster/MsClusterAlgorithm.cpp  
src/PepNovo/DeNovoSolutions.cpp      
src/PepNovo/PeptideRankScorer.cpp
util.cpp
peptide_spectrum_score.cpp
)

add_executable(Cycloquest_html cycloquest_html.cpp)
target_link_libraries(Cycloquest_html all_lib)


