/// <summary>
/// Runs the MultiAlign analysis
/// </summary>
public void PerformMultiAlignAnalysis(DatasetInformation baselineDataset,
IEnumerable <DatasetInformation> aligneeDatasets,
LcmsFeatureFindingOptions featureFindingOptions,
MsFeatureFilteringOptions msFilterOptions,
LcmsFeatureFilteringOptions lcmsFilterOptions,
SpectralOptions peptideOptions,
MultiAlignCore.Algorithms.FeatureFinding.IFeatureFinder featureFinder,
IFeatureAligner <IEnumerable <UMCLight>,
IEnumerable <UMCLight>,
AlignmentData> aligner,
IClusterer <UMCLight, UMCClusterLight> clusterer,
string matchPath,
string errorPath)
{
UpdateStatus("Loading baseline features.");
var msFeatures = UmcLoaderFactory.LoadMsFeatureData(baselineDataset.Features.Path);
msFeatures = LcmsFeatureFilters.FilterMsFeatures(msFeatures, msFilterOptions);
// Load the baseline reference set
using (var rawProviderX = new InformedProteomicsReader())
{
rawProviderX.AddDataFile(baselineDataset.RawFile.Path, 0);
UpdateStatus("Creating Baseline LCMS Features.");
var baselineFeatures = featureFinder.FindFeatures(msFeatures,
featureFindingOptions,
rawProviderX);
LinkPeptidesToFeatures(baselineDataset.Sequence.Path, baselineFeatures, peptideOptions.Fdr,
peptideOptions.IdScore);
var providerX = new CachedFeatureSpectraProvider(rawProviderX, baselineFeatures);
// Then load the alignee dataset
foreach (var dataset in aligneeDatasets)
{
var aligneeMsFeatures = UmcLoaderFactory.LoadMsFeatureData(dataset.Features.Path);
aligneeMsFeatures = LcmsFeatureFilters.FilterMsFeatures(aligneeMsFeatures, msFilterOptions);
using (var rawProviderY = new InformedProteomicsReader())
{
rawProviderY.AddDataFile(dataset.RawFile.Path, 0);
UpdateStatus("Finding alignee features");
var aligneeFeatures = featureFinder.FindFeatures(aligneeMsFeatures,
featureFindingOptions,
rawProviderY);
LinkPeptidesToFeatures(dataset.Sequence.Path, aligneeFeatures, peptideOptions.Fdr,
peptideOptions.IdScore);
var providerY = new CachedFeatureSpectraProvider(rawProviderY, aligneeFeatures);
// cluster before we do anything else....
var allFeatures = new List <UMCLight>();
allFeatures.AddRange(baselineFeatures);
allFeatures.AddRange(aligneeFeatures);
foreach (var feature in allFeatures)
{
feature.Net = feature.Net;
feature.MassMonoisotopicAligned = feature.MassMonoisotopic;
}
// This tells us the differences before we align.
var clusters = clusterer.Cluster(allFeatures);
var preAlignment = AnalyzeClusters(clusters);
aligner.AligneeSpectraProvider = providerY;
aligner.BaselineSpectraProvider = providerX;
UpdateStatus("Aligning data");
// Aligner data
var data = aligner.Align(baselineFeatures, aligneeFeatures);
var matches = data.Matches;
WriteErrors(errorPath, matches);
// create anchor points for LCMSWarp alignment
var massPoints = new List <RegressionPoint>();
var netPoints = new List <RegressionPoint>();
foreach (var match in matches)
{
var massError = FeatureLight.ComputeMassPPMDifference(match.AnchorPointX.Mz,
match.AnchorPointY.Mz);
var netError = match.AnchorPointX.Net - match.AnchorPointY.Net;
var massPoint = new RegressionPoint(match.AnchorPointX.Mz, 0, massError, netError);
massPoints.Add(massPoint);
var netPoint = new RegressionPoint(match.AnchorPointX.Net, 0, massError, netError);
netPoints.Add(netPoint);
}
foreach (var feature in allFeatures)
{
feature.UmcCluster = null;
feature.ClusterId = -1;
}
// Then cluster after alignment!
UpdateStatus("clustering data");
clusters = clusterer.Cluster(allFeatures);
var postAlignment = AnalyzeClusters(clusters);
UpdateStatus("Note\tSame\tDifferent");
UpdateStatus(string.Format("Pre\t{0}\t{1}", preAlignment.SameCluster,
preAlignment.DifferentCluster));
UpdateStatus(string.Format("Post\t{0}\t{1}", postAlignment.SameCluster,
postAlignment.DifferentCluster));
SaveMatches(matchPath, matches);
}
}
}
DeRegisterProgressNotifier(aligner);
DeRegisterProgressNotifier(featureFinder);
DeRegisterProgressNotifier(clusterer);
}
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);
}
}
}
}
