/// <summary>
/// Builds the feature aligner.
/// </summary>
public void BuildAligner(LcmsWarpAlignmentOptions options, SpectralOptions spectralOptions)
{
m_provider.DatasetAligner = FeatureAlignerFactory.CreateDatasetAligner(options.AlignmentAlgorithmType, options,
spectralOptions);
m_provider.DatabaseAligner = FeatureAlignerFactory.CreateDatabaseAligner(options.AlignmentAlgorithmType, options,
spectralOptions);
}
public void TestClustering(
string directory,
string outputPath,
FeatureAlignmentType alignmentType,
LcmsFeatureClusteringAlgorithmType clusterType)
{
var matchPath = string.Format("{0}.txt", outputPath);
var errorPath = string.Format("{0}-errors.txt", outputPath);
// 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);
// Setup our alignment options
var alignmentOptions = new AlignmentOptions();
var spectralOptions = new SpectralOptions
{
ComparerType = SpectralComparison.CosineDotProduct,
Fdr = .01,
IdScore = 1e-09,
MzBinSize = .5,
MzTolerance = .5,
NetTolerance = .1,
RequiredPeakCount = 32,
SimilarityCutoff = .75,
TopIonPercent = .8
};
// 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
};
// Create our algorithms
var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased);
var aligner = FeatureAlignerFactory.CreateDatasetAligner(alignmentType,
alignmentOptions.LCMSWarpOptions,
spectralOptions);
var clusterer = ClusterFactory.Create(clusterType);
clusterer.Parameters = new FeatureClusterParameters <UMCLight>
{
Tolerances = featureTolerances
};
RegisterProgressNotifier(aligner);
RegisterProgressNotifier(finder);
RegisterProgressNotifier(clusterer);
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
};
for (var i = 0; i < 1; i++)
{
var aligneeDatasets = datasets.Where((t, j) => j != i).ToList();
PerformMultiAlignAnalysis(datasets[0],
aligneeDatasets,
featureFindingOptions,
msFilterOptions,
lcmsFilters,
spectralOptions,
finder,
aligner,
clusterer,
matchPath,
errorPath);
}
}
public void GenerateClusterAlignmentStatistics(string relativeDatabasePath,
string relativeName,
string name,
FeatureAlignmentType alignmentType,
LcmsFeatureClusteringAlgorithmType clusterType)
{
var databasePath = GetPath(relativeDatabasePath);
var outputPath = GetOutputPath(relativeName);
if (!Directory.Exists(outputPath))
{
Directory.CreateDirectory(outputPath);
}
// Connect to the NHibernate database
var providers = DataAccessFactory.CreateDataAccessProviders(databasePath, false);
// Setup our alignment options
var alignmentOptions = new AlignmentOptions();
var spectralOptions = new SpectralOptions
{
ComparerType = SpectralComparison.CosineDotProduct,
Fdr = .01,
IdScore = 1e-09,
MzBinSize = .5,
MzTolerance = .5,
NetTolerance = .1,
RequiredPeakCount = 32,
SimilarityCutoff = .75,
TopIonPercent = .8
};
// Options setup
var instrumentOptions = InstrumentPresetFactory.Create(InstrumentPresets.LtqOrbitrap);
var featureTolerances = new FeatureTolerances
{
Mass = instrumentOptions.Mass + 6,
Net = instrumentOptions.NetTolerance,
DriftTime = instrumentOptions.DriftTimeTolerance
};
UpdateStatus("Retrieving all datasets for test.");
var datasets = providers.DatasetCache.FindAll();
// Create our algorithms
var aligner = FeatureAlignerFactory.CreateDatasetAligner(alignmentType,
alignmentOptions.LCMSWarpOptions,
spectralOptions);
var clusterer = ClusterFactory.Create(clusterType);
clusterer.Parameters = new FeatureClusterParameters <UMCLight>
{
Tolerances = featureTolerances
};
RegisterProgressNotifier(aligner);
RegisterProgressNotifier(clusterer);
for (var i = 0; i < datasets.Count - 1; i++)
{
var matchPath = string.Format("{0}-{1}-matches.txt", name, i);
var errorPath = string.Format("{0}-{1}-errors.txt", name, i);
matchPath = Path.Combine(outputPath, matchPath);
errorPath = Path.Combine(outputPath, errorPath);
var aligneeDataset = datasets[i + 1];
var baselineDataset = datasets[i];
// Load the baseline reference set
using (var rawProviderX = new InformedProteomicsReader())
{
rawProviderX.AddDataFile(baselineDataset.RawFile.Path, 0);
// Load the baseline reference set
using (var rawProviderY = new InformedProteomicsReader())
{
rawProviderY.AddDataFile(aligneeDataset.RawFile.Path, 0);
var baselineFeatures = RetrieveFeatures(baselineDataset.DatasetId, providers);
var aligneeFeatures = RetrieveFeatures(aligneeDataset.DatasetId, providers);
var providerX = new CachedFeatureSpectraProvider(rawProviderX, baselineFeatures);
var providerY = new CachedFeatureSpectraProvider(rawProviderY, aligneeFeatures);
AlignDatasets(baselineFeatures,
aligneeFeatures,
providerX,
providerY,
aligner,
clusterer,
matchPath,
errorPath);
}
}
}
}