/// <summary>
/// Builds a peak matcher object.
/// </summary>
public void BuildPeakMatcher(MultiAlignAnalysisOptions options)
{
var tolerances = new FeatureMatcherTolerances();
var stanleyMatcher = new STACAdapter<UMCClusterLight>
{
Options =
{
HistogramBinWidth = options.StacOptions.HistogramBinWidth,
HistogramMultiplier = options.StacOptions.HistogramMultiplier,
ShiftAmount = options.StacOptions.ShiftAmount,
ShouldCalculateHistogramFDR = options.StacOptions.ShouldCalculateHistogramFDR,
ShouldCalculateShiftFDR = options.StacOptions.ShouldCalculateShiftFDR,
ShouldCalculateSLiC = options.StacOptions.ShouldCalculateSLiC,
ShouldCalculateSTAC = options.StacOptions.ShouldCalculateSTAC,
UseDriftTime = options.StacOptions.UseDriftTime,
UseEllipsoid = options.StacOptions.UseEllipsoid,
UsePriors = options.StacOptions.UsePriors
}
};
tolerances.DriftTimeTolerance = Convert.ToSingle(options.StacOptions.DriftTimeTolerance);
tolerances.MassTolerancePPM = options.StacOptions.MassTolerancePPM;
tolerances.NETTolerance = options.StacOptions.NETTolerance;
tolerances.Refined = options.StacOptions.Refined;
stanleyMatcher.Options.UserTolerances = tolerances;
m_provider.PeakMatcher = stanleyMatcher;
}
/// <summary>
/// Default constructor for a MultiAlign analysis object.
/// </summary>
public MultiAlignAnalysis()
{
// Meta Data Information about the analysis and datasets.
MetaData = new AnalysisMetaData {AnalysisName = string.Empty};
Options = new MultiAlignAnalysisOptions();
MassTagDatabase = new MassTagDatabase();
// Alignment options and data.
AlignmentData = new List<classAlignmentData>();
MatchResults = null;
}
public ClusterSettingsViewModel(MultiAlignAnalysis analysis, IProgress<int> progressReporter = null)
{
this.analysis = analysis;
this.options = analysis.Options;
this.builder = new AlgorithmBuilder();
this.ClusterFeaturesCommand = new RelayCommand(this.AsyncClusterFeatures);
this.DisplayClustersCommand = new RelayCommand(this.DisplayFeatures);
this.DistanceMetrics = new ObservableCollection<DistanceMetric>();
Enum.GetValues(typeof(DistanceMetric)).Cast<DistanceMetric>().ToList().ForEach(x => this.DistanceMetrics.Add(x));
this.CentroidRepresentations = new ObservableCollection<ClusterCentroidRepresentation>();
Enum.GetValues(typeof(ClusterCentroidRepresentation)).Cast<ClusterCentroidRepresentation>().ToList().ForEach(x => this.CentroidRepresentations.Add(x));
this.ClusteringMethods = new ObservableCollection<LcmsFeatureClusteringAlgorithmType>();
Enum.GetValues(typeof(LcmsFeatureClusteringAlgorithmType)).Cast<LcmsFeatureClusteringAlgorithmType>().ToList().ForEach(x => this.ClusteringMethods.Add(x));
}
private void LoadExistingParameters()
{
try
{
//TODO: Replace with OOKI dialogs
var result = m_dialog.ShowDialog();
if (result != null && result.Value)
{
var reader = new JsonReader<MultiAlignAnalysisOptions>();
m_options = reader.Read(m_dialog.FileName);
UpdateOptions();
}
}
//TODO: Replace with appropriate exception handling
catch (Exception)
{
//TODO: Display the error
}
}
public AnalysisOptionsViewModel(MultiAlignAnalysisOptions options)
{
m_options = options;
ClusteringAlgorithms = new ObservableCollection<LcmsFeatureClusteringAlgorithmType>();
AlignmentAlgorithms = new ObservableCollection<FeatureAlignmentType>();
FeatureFindingAlgorithms = new ObservableCollection<FeatureFinderType>();
UpdateOptions();
InstrumentPresets = new ObservableCollection<InstrumentPresetViewModel>();
ExperimentPresets = new ObservableCollection<ExperimentPresetViewModel>();
TimeOptions = new ObservableCollection<string>();
var presets = new Dictionary<string, bool>();
foreach (var preset in ExperimentPresetFactory.Create())
{
ExperimentPresets.Add(preset);
if (!presets.ContainsKey(preset.InstrumentPreset.Name))
{
presets.Add(preset.InstrumentPreset.Name, false);
InstrumentPresets.Add(preset.InstrumentPreset);
}
}
foreach (var preset in InstrumentPresetFactory.Create())
{
if (!presets.ContainsKey(preset.Name))
{
InstrumentPresets.Add(preset);
}
}
TimeOptions.Add("Minutes");
TimeOptions.Add("Scans");
SelectedPreset = InstrumentPresets[0];
SelectedExperimentPreset = ExperimentPresets[0];
TreatAsTimeOrScan = TimeOptions[0];
m_saveDialog = new SaveFileDialog();
m_dialog = new OpenFileDialog
{
Filter = Resources.MultiAlignParameterFileFilter
};
m_saveDialog.Filter = Resources.MultiAlignParameterFileFilter;
ShowAdvancedWindowCommand = new BaseCommand(ShowAdvancedWindow);
SaveOptionsCommand = new BaseCommand(SaveCurrentParameters);
LoadExistingCommand = new BaseCommand(LoadExistingParameters);
Enum.GetValues(typeof (LcmsFeatureClusteringAlgorithmType))
.Cast<LcmsFeatureClusteringAlgorithmType>()
.ToList()
.ForEach(x => ClusteringAlgorithms.Add(x));
Enum.GetValues(typeof (FeatureAlignmentType))
.Cast<FeatureAlignmentType>()
.ToList()
.ForEach(x => AlignmentAlgorithms.Add(x));
Enum.GetValues(typeof (FeatureFinderType))
.Cast<FeatureFinderType>()
.ToList()
.ForEach(x => FeatureFindingAlgorithms.Add(x));
}
/// <summary>
/// Returns the list of algorithms post build.
/// </summary>
/// <returns></returns>
public AlgorithmProvider GetAlgorithmProvider(MultiAlignAnalysisOptions options)
{
BuildClusterer(LcmsFeatureClusteringAlgorithmType.AverageLinkage);
BuildAligner(options.AlignmentOptions.LCMSWarpOptions, options.SpectralOptions);
BuildPeakMatcher(options);
return m_provider;
}