public void Setup() { NHibernateUtil.CreateDatabase("test.db3"); }
public void CreateFeatureDatabase(string directoryPath, string databasePath) { var directory = GetPath(directoryPath); databasePath = GetPath(databasePath); // Loads the supported MultiAlign types var supportedTypes = DatasetLoader.SupportedFileTypes; var extensions = new List <string>(); supportedTypes.ForEach(x => extensions.Add("*" + x.Extension)); // Find our datasets var datasetLoader = new DatasetLoader(); var datasets = datasetLoader.GetValidDatasets(directory, extensions, SearchOption.TopDirectoryOnly); // Options setup var instrumentOptions = InstrumentPresetFactory.Create(InstrumentPresets.LtqOrbitrap); var featureTolerances = new FeatureTolerances { Mass = instrumentOptions.Mass + 6, Net = instrumentOptions.NetTolerance, DriftTime = instrumentOptions.DriftTimeTolerance }; var featureFindingOptions = new LcmsFeatureFindingOptions(featureTolerances) { MaximumNetRange = .002, MaximumScanRange = 50 }; var lcmsFilters = new LcmsFeatureFilteringOptions { FeatureLengthRangeScans = new FilterRange(50, 300) }; var msFilterOptions = new MsFeatureFilteringOptions { MinimumIntensity = 5000, ChargeRange = new FilterRange(1, 6), ShouldUseChargeFilter = true, ShouldUseDeisotopingFilter = true, ShouldUseIntensityFilter = true }; var spectralOptions = new SpectralOptions { ComparerType = SpectralComparison.CosineDotProduct, Fdr = .01, IdScore = 1e-09, MzBinSize = .5, MzTolerance = .5, NetTolerance = .1, RequiredPeakCount = 32, SimilarityCutoff = .75, TopIonPercent = .8 }; var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased); NHibernateUtil.CreateDatabase(databasePath); // Synchronization and IO for serializing all data to the database. var providers = DataAccessFactory.CreateDataAccessProviders(databasePath, true); var cache = new FeatureLoader { Providers = providers }; var datasetId = 0; foreach (var dataset in datasets) { dataset.DatasetId = datasetId++; var features = FindFeatures(dataset, featureFindingOptions, msFilterOptions, lcmsFilters, spectralOptions, finder); cache.CacheFeatures(features); } providers.DatasetCache.AddAll(datasets); }