/// <summary>
/// Default constructor.
/// </summary>
public AlgorithmBuilder()
{
m_provider = new AlgorithmProvider();
}
public void ClusterFeatures()
{
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;
// This just tells us whether we are using mammoth memory partitions or not.
var clusterCount = 0;
var providers = this.analysis.DataProviders;
// Here we see if we need to separate the charge...
// IMS is said to require charge separation
if (!this.analysis.Options.LcmsClusteringOptions.ShouldSeparateCharge)
{
var features = this.featureCache.FindAll();
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.UpdateAll(features);
this.analysis.Clusters = clusters;
}
else
{
var maxChargeState = this.featureCache.FindMaxCharge();
/*
* Here we cluster all charge states separately. Probably IMS Data.
*/
for (var chargeState = 1; chargeState <= maxChargeState; chargeState++)
{
var features = this.featureCache.FindByCharge(chargeState);
if (features.Count < 1)
{
break;
}
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;
}
}
this.analysis.DataProviders.ClusterCache.AddAll(clusters);
this.analysis.DataProviders.FeatureCache.UpdateAll(features);
}
this.analysis.Clusters = this.analysis.DataProviders.ClusterCache.FindAll();
}
MessageBox.Show("Working Command");
}
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>
/// Default constructor.
/// </summary>
public MultiAlignAnalysisProcessor()
{
m_algorithms = null;
CreateAnalysisMethodMap();
}
/// <summary>
/// Default constructor.
/// </summary>
public MultiAlignAnalysisProcessor()
{
m_algorithms = null;
CreateAnalysisMethodMap();
}
/// <summary>
/// Default constructor.
/// </summary>
public AlgorithmBuilder()
{
m_provider = new AlgorithmProvider();
}