/// <summary>
/// Load the data from the dataset information objects to the cache at the analysis Path
/// </summary>
private void PerformDataLoadAndAlignment(AnalysisConfig config)
{
UmcLoaderFactory.Status += UMCLoaderFactory_Status;
UpdateStatus("Loading data.");
var analysisOptions = config.Analysis.Options;
var datasets = config.Analysis.MetaData.Datasets.ToList();
var lcmsFilterOptions = analysisOptions.LcmsFilteringOptions;
var msFilterOptions = analysisOptions.MsFilteringOptions;
var baselineDataset = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineDataset,
msFilterOptions,
analysisOptions.LcmsFindingOptions,
lcmsFilterOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
var providers = config.Analysis.DataProviders;
var featureCache = new FeatureLoader
{
Providers = providers
};
RegisterProgressNotifier(featureCache);
MassTagDatabase database = null;
if (config.Analysis.MassTagDatabase != null)
database = new MassTagDatabase(config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.MassTagObservationCount);
SingletonDataProviders.Providers = config.Analysis.DataProviders;
foreach (var dataset in datasets)
{
if (dataset.IsBaseline)
continue;
var features = featureCache.LoadDataset(dataset,
analysisOptions.MsFilteringOptions,
analysisOptions.LcmsFindingOptions,
analysisOptions.LcmsFilteringOptions);
features = AlignDataset(features,
baselineFeatures,
database,
dataset,
baselineDataset);
featureCache.CacheFeatures(features);
}
UmcLoaderFactory.Status -= UMCLoaderFactory_Status;
}
/// <summary>
/// Loads baseline data for alignment.
/// </summary>
private IList<UMCLight> LoadBaselineData(DatasetInformation baselineInfo,
MsFeatureFilteringOptions msFilterOptions,
LcmsFeatureFindingOptions lcmsFindingOptions,
LcmsFeatureFilteringOptions lcmsFilterOptions,
FeatureDataAccessProviders dataProviders,
MassTagDatabase database,
bool shouldUseMassTagDbAsBaseline)
{
IList<UMCLight> baselineFeatures = null;
UpdateStatus("Loading baseline features.");
if (!shouldUseMassTagDbAsBaseline)
{
if (baselineInfo == null)
{
throw new Exception("The baseline dataset was never set.");
}
var cache = new FeatureLoader
{
Providers = dataProviders
};
RegisterProgressNotifier(cache);
UpdateStatus("Loading baseline features from " + baselineInfo.DatasetName + " for alignment.");
baselineFeatures = cache.LoadDataset(baselineInfo,
msFilterOptions,
lcmsFindingOptions,
lcmsFilterOptions);
cache.CacheFeatures(baselineFeatures);
if (BaselineFeaturesLoaded != null)
{
BaselineFeaturesLoaded(this,
new BaselineFeaturesLoadedEventArgs(baselineInfo, baselineFeatures.ToList()));
}
DeRegisterProgressNotifier(cache);
}
else
{
if (database == null)
throw new NullReferenceException(
"The mass tag database has to have data in it if it's being used for drift time alignment.");
UpdateStatus("Setting baseline features for post drift time alignment from mass tag database.");
var tags = FeatureDataConverters.ConvertToUMC(database.MassTags);
if (BaselineFeaturesLoaded == null)
return tags;
if (tags != null)
BaselineFeaturesLoaded(this, new BaselineFeaturesLoadedEventArgs(null, tags.ToList(), database));
}
return baselineFeatures;
}
