/// <summary>
/// Finds features given a dataset
/// </summary>
private IList <UMCLight> FindFeatures(DatasetInformation information,
LcmsFeatureFindingOptions featureFindingOptions,
MsFeatureFilteringOptions msFilterOptions,
LcmsFeatureFilteringOptions lcmsFilterOptions,
SpectralOptions peptideOptions,
MultiAlignCore.Algorithms.FeatureFinding.IFeatureFinder featureFinder)
{
UpdateStatus("Loading baseline features.");
var msFeatures = UmcLoaderFactory.LoadMsFeatureData(information.Features.Path);
msFeatures = LcmsFeatureFilters.FilterMsFeatures(msFeatures, msFilterOptions);
// Load the baseline reference set
using (var rawProviderX = RawLoaderFactory.CreateFileReader(information.RawFile.Path))
{
rawProviderX.AddDataFile(information.RawFile.Path, 0);
UpdateStatus("Creating LCMS Features.");
var features = featureFinder.FindFeatures(msFeatures,
featureFindingOptions,
rawProviderX);
features = LcmsFeatureFilters.FilterFeatures(features, lcmsFilterOptions, information.ScanTimes);
var datasetId = information.DatasetId;
foreach (var feature in features)
{
var lightEntry = new List <MSFeatureLight>();
feature.GroupId = datasetId;
foreach (var msFeature in feature.MsFeatures)
{
msFeature.GroupId = datasetId;
foreach (var msmsFeature in msFeature.MSnSpectra)
{
msmsFeature.GroupId = datasetId;
foreach (var peptide in msmsFeature.Peptides)
{
peptide.GroupId = datasetId;
}
}
if (msFeature.MSnSpectra.Count > 0)
{
lightEntry.Add(msFeature);
}
}
// We are doing this so that we dont have a ton of MS features in the database
feature.MsFeatures.Clear();
feature.MsFeatures.AddRange(lightEntry);
}
LinkPeptidesToFeatures(information.SequenceFile.Path,
features,
peptideOptions.Fdr,
peptideOptions.IdScore);
DeRegisterProgressNotifier(featureFinder);
return(features);
}
}
/// <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);
}