/// <summary>
/// Constructor
/// </summary>
public MultiAlignAnalysisOptions()
{
InstrumentTolerances = new FeatureTolerances();
MassTagDatabaseOptions = new MassTagDatabaseOptions();
MsFilteringOptions = new MsFeatureFilteringOptions();
LcmsFindingOptions = new LcmsFeatureFindingOptions(InstrumentTolerances);
LcmsFilteringOptions = new LcmsFeatureFilteringOptions();
LcmsFilteringOptions.TreatAsTimeNotScan = true;
LcmsFilteringOptions.FeatureLengthRange = new FilterRange(0, 20);
AlignmentOptions = new AlignmentOptions();
LcmsClusteringOptions = new LcmsClusteringOptions(InstrumentTolerances);
StacOptions = new StacOptions();
HasMsMs = false;
UsedIonMobility = false;
}
/// <summary>
/// Constructor
/// </summary>
public MultiAlignAnalysisOptions()
{
DataLoadOptions = new DataLoadingOptions();
InstrumentTolerances = new FeatureTolerances();
MassTagDatabaseOptions = new MassTagDatabaseOptions();
MsFilteringOptions = new MsFeatureFilteringOptions();
LcmsFindingOptions = new LcmsFeatureFindingOptions(InstrumentTolerances);
LcmsFilteringOptions = new LcmsFeatureFilteringOptions
{
FilterOnMinutes = true,
FeatureLengthRangeMinutes = new FilterRange(0, 20),
MinimumDataPoints = 3,
FeatureLengthRangeScans = new FilterRange(0, 2000)
};
AlignmentOptions = new AlignmentOptions();
LcmsClusteringOptions = new LcmsClusteringOptions(InstrumentTolerances);
StacOptions = new StacOptions();
HasMsMs = false;
UsedIonMobility = false;
this.ClusterPostProcessingoptions = new ClusterPostProcessingOptions();
}
internal void ClusterFeatures(IProgress <ProgressData> workflowProgress = null)
{
var taskBarProgress = TaskBarProgress.GetInstance();
taskBarProgress.ShowProgress(this, true);
workflowProgress = workflowProgress ?? new Progress <ProgressData>();
IProgress <ProgressData> internalProgress = new Progress <ProgressData>(pd =>
{
this.progress.Report((int)pd.Percent);
this.ProgressPercent = pd.Percent;
taskBarProgress.SetProgress(this, pd.Percent);
workflowProgress.Report(pd);
});
this.algorithms = this.builder.GetAlgorithmProvider(this.options);
var clusterer = this.algorithms.Clusterer;
clusterer.Parameters = LcmsClusteringOptions.ConvertToOmics(this.options.LcmsClusteringOptions);
this.featureCache = this.analysis.DataProviders.FeatureCache;
if (clusterer is PromexClusterer)
{
var promexClusterer = clusterer as PromexClusterer;
promexClusterer.Readers = this.analysis.DataProviders.ScanSummaryProviderCache;
}
foreach (var dataset in this.Datasets)
{
if (dataset.FeaturesFound)
{
dataset.DatasetState = DatasetInformationViewModel.DatasetStates.Clustering;
}
}
ThreadSafeDispatcher.Invoke(this.ClusterFeaturesCommand.RaiseCanExecuteChanged);
ThreadSafeDispatcher.Invoke(this.DisplayClustersCommand.RaiseCanExecuteChanged);
this.ShouldShowProgress = true;
var progData = new ProgressData(internalProgress);
var clusterProgress = new Progress <ProgressData>(pd => progData.Report(pd.Percent));
this.analysis.DataProviders.DatabaseLock.EnterWriteLock();
DatabaseIndexer.IndexClustersDrop(NHibernateUtil.Path);
this.analysis.DataProviders.ClusterCache.ClearAllClusters();
this.analysis.DataProviders.DatabaseLock.ExitWriteLock();
// The id for a cluster - keep track here to avoid duplicates when separating by charge.
var clusterCount = 0;
// Here we see if we need to separate the charge...
// IMS is said to require charge separation
if (!this.analysis.Options.LcmsClusteringOptions.ShouldSeparateCharge)
{
progData.StepRange(45);
var features = new List <UMCLight>();
var i = 0;
var datasets = this.Datasets.Where(ds => ds.FeaturesFound).ToList();
foreach (var dataset in datasets)
{
this.analysis.DataProviders.DatabaseLock.EnterReadLock();
features.AddRange(this.featureCache.FindByDatasetId(dataset.DatasetId));
this.analysis.DataProviders.DatabaseLock.ExitReadLock();
progData.Report(++i, datasets.Count);
}
progData.StepRange(100);
ClusterGroupOfFeatures(clusterer, features, ref clusterCount, clusterProgress);
}
else
{
var maxChargeState = this.featureCache.FindMaxCharge();
// Here we cluster all charge states separately. Probably IMS Data.
for (var chargeState = 1; chargeState <= maxChargeState; chargeState++)
{
var maxPercent = ((100.0 * chargeState) / maxChargeState);
// TODO: Add restriction by selected dataset ids?
var features = this.featureCache.FindByCharge(chargeState);
if (features.Count < 1)
{
continue;
}
progData.StepRange(maxPercent);
ClusterGroupOfFeatures(clusterer, features, ref clusterCount, clusterProgress);
}
this.analysis.Clusters = this.analysis.DataProviders.ClusterCache.FindAll();
}
this.analysis.DataProviders.DatabaseLock.EnterWriteLock();
DatabaseIndexer.IndexClusters(NHibernateUtil.Path);
this.analysis.DataProviders.DatabaseLock.ExitWriteLock();
foreach (var dataset in this.Datasets)
{
if (dataset.DatasetState == DatasetInformationViewModel.DatasetStates.PersistingClusters)
{
dataset.DatasetState = DatasetInformationViewModel.DatasetStates.Clustered;
}
}
try
{
// Write to file
this.WriteClusterData(string.Format("{0}_crosstab.tsv", this.analysis.AnalysisName), this.analysis.Clusters);
}
catch (Exception ex)
{
var errMsg = "Error writing results to text file: " + ex.Message;
Logger.PrintMessage(errMsg);
// Todo: Add this: if (!GlobalSettings.AutomatedAnalysisMode)
MessageBox.Show(errMsg);
}
ThreadSafeDispatcher.Invoke(this.ClusterFeaturesCommand.RaiseCanExecuteChanged);
ThreadSafeDispatcher.Invoke(this.DisplayClustersCommand.RaiseCanExecuteChanged);
taskBarProgress.ShowProgress(this, false);
this.ShouldShowProgress = false;
}
/// <summary>
/// Performs clustering of LCMS Features
/// </summary>
public void PerformLcmsFeatureClustering(AnalysisConfig config)
{
var analysis = config.Analysis;
var clusterer = m_algorithms.Clusterer;
RegisterProgressNotifier(clusterer);
UpdateStatus("Using Cluster Algorithm: " + clusterer);
clusterer.Parameters = LcmsClusteringOptions.ConvertToOmics(analysis.Options.LcmsClusteringOptions);
// This just tells us whether we are using mammoth memory partitions or not.
var featureCache = config.Analysis.DataProviders.FeatureCache;
var clusterCount = 0;
var providers = config.Analysis.DataProviders;
// Here we see if we need to separate the charge...
// IMS is said to require charge separation
if (!analysis.Options.LcmsClusteringOptions.ShouldSeparateCharge)
{
UpdateStatus("Clustering features from all charge states.");
UpdateStatus("Retrieving features for clustering from cache.");
var features = featureCache.FindAll();
UpdateStatus(string.Format("Clustering {0} features. ", features.Count));
var clusters = new List <UMCClusterLight>();
clusters = clusterer.Cluster(features, clusters);
foreach (var cluster in clusters)
{
cluster.Id = clusterCount++;
cluster.UmcList.ForEach(x => x.ClusterId = cluster.Id);
// Updates the cluster with statistics
foreach (var feature in cluster.UmcList)
{
cluster.MsMsCount += feature.MsMsCount;
cluster.IdentifiedSpectraCount += feature.IdentifiedSpectraCount;
}
}
providers.ClusterCache.AddAll(clusters);
providers.FeatureCache.UpdateAllStateless(features);
config.Analysis.Clusters = clusters;
UpdateStatus(string.Format("Found {0} clusters.", clusters.Count));
if (FeaturesClustered != null)
{
FeaturesClustered(this, new FeaturesClusteredEventArgs(clusters));
}
}
else
{
var maxChargeState = featureCache.FindMaxCharge();
/*
* Here we cluster all charge states separately. Probably IMS Data.
*/
UpdateStatus("Clustering charge states individually.");
for (var chargeState = 1; chargeState <= maxChargeState; chargeState++)
{
var features = featureCache.FindByCharge(chargeState);
if (features.Count < 1)
{
UpdateStatus(string.Format("No features found for charge state {0}. Stopping clustering",
chargeState));
break;
}
UpdateStatus(
string.Format("Retrieved and is clustering {0} features from charge state {1}.",
features.Count, chargeState));
var clusters = clusterer.Cluster(features);
foreach (var cluster in clusters)
{
cluster.Id = clusterCount++;
cluster.UmcList.ForEach(x => x.ClusterId = cluster.Id);
// Updates the cluster with statistics
foreach (var feature in cluster.Features)
{
cluster.MsMsCount += feature.MsMsCount;
cluster.IdentifiedSpectraCount += feature.IdentifiedSpectraCount;
}
}
config.Analysis.DataProviders.ClusterCache.AddAll(clusters);
config.Analysis.DataProviders.FeatureCache.UpdateAllStateless(features);
UpdateStatus(string.Format("Found {0} clusters.", clusters.Count));
if (FeaturesClustered != null)
{
FeaturesClustered(this, new FeaturesClusteredEventArgs(clusters, chargeState));
}
}
config.Analysis.Clusters = config.Analysis.DataProviders.ClusterCache.FindAll();
}
DeRegisterProgressNotifier(clusterer);
UpdateStatus(string.Format("Finished clustering. Found {0} total clusters.", clusterCount));
}
