/// <summary>
/// Aligns all of the datasets.
/// </summary>
public void PerformAlignment(AnalysisConfig config)
{
UpdateStatus("Performing Alignment");
// Connect to database of features.
var featureCache = config.Analysis.DataProviders.FeatureCache;
var options = config.Analysis.Options;
// Load the baseline data.
var baselineInfo = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineInfo,
options.MsFilteringOptions,
options.LcmsFindingOptions,
options.LcmsFilteringOptions,
options.DataLoadOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
// Create the alignment cache and clear it.
var alignmentCache = new AlignmentDAOHibernate();
alignmentCache.ClearAll();
//config.Analysis.Options.AlignmentOptions
foreach (var datasetInfo in config.Analysis.MetaData.Datasets)
{
if (!datasetInfo.IsBaseline)
{
UpdateStatus("Retrieving data from " + datasetInfo.DatasetName + " for alignment.");
var features = featureCache.FindByDatasetId(datasetInfo.DatasetId) as IList <UMCLight>;
features = AlignDataset(features,
baselineFeatures,
config.Analysis.MassTagDatabase,
datasetInfo,
baselineInfo);
featureCache.UpdateAllStateless(features);
// This dataset is done!
if (FeaturesLoaded != null)
{
FeaturesLoaded(this, new FeaturesLoadedEventArgs(datasetInfo, features));
}
}
else
{
config.Analysis.AlignmentData.Add(null);
}
}
}
private void AlignToBaseline()
{
if (this.SelectedBaseline != null && this.SelectedBaseline.Dataset.FeaturesFound)
{
//Update algorithms and providers
this.featureCache.Providers = this.analysis.DataProviders;
this.algorithms = this.builder.GetAlgorithmProvider(this.analysis.Options);
this.aligner.m_algorithms = this.algorithms;
var baselineFeatures = this.featureCache.LoadDataset(this.selectedBaseline.Dataset, this.analysis.Options.MsFilteringOptions,
this.analysis.Options.LcmsFindingOptions, this.analysis.Options.LcmsFilteringOptions);
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
this.SelectedBaseline.IsAligning = true;
var selectedFiles = this.selectedDatasets.Where(file => !file.DoingWork).ToList();
foreach (var file in selectedFiles)
{
file.IsAligning = true;
}
foreach (var file in selectedFiles)
{
ThreadSafeDispatcher.Invoke(() => this.AlignToBaselineCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged());
if (file.Dataset.IsBaseline || !file.FeaturesFound)
{
file.IsAligned = true;
file.IsAligning = false;
continue;
}
var features = this.featureCache.LoadDataset(file.Dataset, this.analysis.Options.MsFilteringOptions,
this.analysis.Options.LcmsFindingOptions, this.analysis.Options.LcmsFilteringOptions);
var alignment = this.aligner.AlignToDataset(ref features, baselineFeatures, file.Dataset, this.selectedBaseline.Dataset);
//Check if there is information from a previous alignment for this dataset. If so, replace it. If not, just add the new one.
var priorAlignment = from x in this.alignmentInformation where x.DatasetID == alignment.DatasetID select x;
if (priorAlignment.Any())
{
this.alignmentInformation.Remove(priorAlignment.Single());
this.alignmentInformation.Add(alignment);
}
else
{
this.alignmentInformation.Add(alignment);
}
this.featureCache.CacheFeatures(features);
file.IsAligned = true;
file.IsAligning = false;
ThreadSafeDispatcher.Invoke(() => this.AlignToBaselineCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged());
}
this.SelectedBaseline.IsAligning = false;
}
else
{
MessageBox.Show("Please select a baseline with detected features.");
}
}
/// <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>
/// Aligns all of the datasets.
/// </summary>
public void PerformAlignment(AnalysisConfig config)
{
UpdateStatus("Performing Alignment");
// Connect to database of features.
var featureCache = config.Analysis.DataProviders.FeatureCache;
var options = config.Analysis.Options;
// Load the baseline data.
var baselineInfo = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineInfo,
options.MsFilteringOptions,
options.LcmsFindingOptions,
options.LcmsFilteringOptions,
config.Analysis.DataProviders,
config.Analysis.MassTagDatabase,
config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB);
// Create the alignment cache and clear it.
var alignmentCache = new AlignmentDAOHibernate();
alignmentCache.ClearAll();
//config.Analysis.Options.AlignmentOptions
foreach (var datasetInfo in config.Analysis.MetaData.Datasets)
{
if (!datasetInfo.IsBaseline)
{
UpdateStatus("Retrieving data from " + datasetInfo.DatasetName + " for alignment.");
var features = featureCache.FindByDatasetId(datasetInfo.DatasetId) as IList<UMCLight>;
features = AlignDataset(features,
baselineFeatures,
config.Analysis.MassTagDatabase,
datasetInfo,
baselineInfo);
featureCache.UpdateAll(features);
// This dataset is done!
if (FeaturesLoaded != null)
FeaturesLoaded(this, new FeaturesLoadedEventArgs(datasetInfo, features));
}
else
{
config.Analysis.AlignmentData.Add(null);
}
}
}
/// <summary>
/// Perform alignment.
/// </summary>
/// <param name="workFlowDatasets">Datasets to run on when being called externally form this view model.</param>
/// <param name="workflowProgress">The progress reporter for when this method is called externally from this view model.</param>
internal void AlignToBaseline(List <DatasetInformationViewModel> workFlowDatasets = null, IProgress <ProgressData> workflowProgress = null)
{
// Use Promiscuous points when aligning to an AMT tag database
// Do not use Promiscuous points when aligning to a baseline dataset
this.analysis.Options.AlignmentOptions.UsePromiscuousPoints = !this.ShouldAlignToBaseline;
// Flag whether we are aligning to an AMT tag database
this.analysis.Options.AlignmentOptions.LCMSWarpOptions.AlignToMassTagDatabase = !this.ShouldAlignToBaseline;
// Show the progress bar
this.ShowAlignmentProgress = true;
var taskBarProgress = TaskBarProgress.GetInstance();
taskBarProgress.ShowProgress(this, true);
// Update algorithms and providers
var featureCache = new FeatureLoader {
Providers = this.analysis.DataProviders
};
this.algorithms = this.builder.GetAlgorithmProvider(this.analysis.Options);
////this.algorithms.DatabaseAligner.Progress += aligner_Progress;
////this.algorithms.DatasetAligner.Progress += aligner_Progress;
this.aligner.m_algorithms = this.algorithms;
var baselineFeatures = new List <UMCLight>();
if (this.ShouldAlignToBaseline)
{
baselineFeatures = featureCache.Providers.FeatureCache.FindByDatasetId(this.selectedBaseline.DatasetId);
this.SelectedBaseline.DatasetState = DatasetInformationViewModel.DatasetStates.Baseline;
var priorAlignment = (from x in this.alignmentInformation where x.DatasetID == this.selectedBaseline.DatasetId select x).ToList();
if (priorAlignment.Any())
{
this.alignmentInformation.Remove(priorAlignment.Single());
}
}
var alignmentData = new AlignmentDAOHibernate();
alignmentData.ClearAll();
var selectedFiles = workFlowDatasets ??
this.Datasets.Where(file => file.IsSelected && !file.DoingWork &&
(this.ShouldAlignToAMT || !file.IsBaseline)).ToList();
foreach (var file in selectedFiles)
{
file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligning;
}
workflowProgress = workflowProgress ?? new Progress <ProgressData>();
IProgress <ProgressData> totalProgress = new Progress <ProgressData>(pd =>
{
this.AlignmentProgress = pd.Percent;
workflowProgress.Report(pd);
taskBarProgress.SetProgress(this, pd.Percent);
});
var totalProgressData = new ProgressData(totalProgress);
DatabaseIndexer.IndexClustersDrop(NHibernateUtil.Path);
DatabaseIndexer.IndexFeaturesDrop(NHibernateUtil.Path);
var i = 1;
foreach (var file in selectedFiles)
{
ThreadSafeDispatcher.Invoke(() => this.AlignCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.SaveAlignmentPlotsCommand.RaiseCanExecuteChanged());
if ((file.Dataset.IsBaseline || !file.FeaturesFound) && this.ShouldAlignToBaseline)
{
file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned;
continue;
}
this.analysis.DataProviders.DatabaseLock.EnterReadLock();
IList <UMCLight> features = featureCache.Providers.FeatureCache.FindByDatasetId(file.DatasetId);
this.analysis.DataProviders.DatabaseLock.ExitReadLock();
AlignmentData alignment;
totalProgressData.StepRange((100.0 * i++) / selectedFiles.Count);
var fileInstance = file;
var datasetProgress =
new Progress <ProgressData>(
pd =>
{
fileInstance.Progress = pd.Percent;
totalProgressData.Report(pd.Percent);
});
if (this.ShouldAlignToBaseline)
{
// Aligning to a baseline dataset
alignment = this.aligner.AlignToDataset(ref features, file.Dataset, baselineFeatures, datasetProgress);
alignment.BaselineIsAmtDB = false;
}
else
{
// Aligning to a database
alignment = this.aligner.AlignToDatabase(ref features, file.Dataset, this.analysis.MassTagDatabase, datasetProgress);
alignment.BaselineIsAmtDB = true;
}
// Check if there is information from a previous alignment for this dataset. If so, replace it. If not, just add the new one.
var priorAlignment = this.alignmentInformation.Where(x => x.DatasetID == alignment.DatasetID).ToList();
if (priorAlignment.Any())
{
this.alignmentInformation.Remove(priorAlignment.Single());
this.alignmentInformation.Add(alignment);
}
else
{
this.alignmentInformation.Add(alignment);
}
file.Dataset.AlignmentData = alignment;
this.analysis.DataProviders.DatabaseLock.EnterWriteLock();
featureCache.CacheFeatures(features);
this.analysis.DataProviders.DatabaseLock.ExitWriteLock();
file.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned;
ThreadSafeDispatcher.Invoke(() => this.AlignCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.DisplayAlignmentCommand.RaiseCanExecuteChanged());
ThreadSafeDispatcher.Invoke(() => this.SaveAlignmentPlotsCommand.RaiseCanExecuteChanged());
file.Progress = 0;
}
if (this.ShouldAlignToBaseline)
{
this.SelectedBaseline.DatasetState = DatasetInformationViewModel.DatasetStates.Aligned;
}
DatabaseIndexer.IndexFeatures(NHibernateUtil.Path);
taskBarProgress.ShowProgress(this, false);
this.ShowAlignmentProgress = false;
this.AlignmentProgress = 0;
}
/// <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 dataLoadOptions = analysisOptions.DataLoadOptions;
var baselineDataset = config.Analysis.MetaData.BaselineDataset;
var baselineFeatures = LoadBaselineData(baselineDataset,
msFilterOptions,
analysisOptions.LcmsFindingOptions,
lcmsFilterOptions,
dataLoadOptions,
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,
analysisOptions.DataLoadOptions,
m_scanSummaryProviderCache,
m_identificationsProvider);
features = AlignDataset(features,
baselineFeatures,
database,
dataset,
baselineDataset);
featureCache.CacheFeatures(features);
}
UmcLoaderFactory.Status -= UMCLoaderFactory_Status;
}
