/// <summary>
/// Finds LCMS Features using the PNNL Omics linkage clustering algorithms.
/// </summary>
public List <UMCLight> FindFeatures(List <MSFeatureLight> rawMsFeatures,
LCMSFeatureFindingOptions options,
ISpectraProvider provider)
{
const ClusterCentroidRepresentation centroidType = ClusterCentroidRepresentation.Mean;
List <UMCLight> features = null;
m_options = options;
m_minScan = int.MaxValue;
m_maxScan = int.MinValue;
foreach (var feature in rawMsFeatures)
{
m_minScan = Math.Min(feature.Scan, m_minScan);
m_maxScan = Math.Max(feature.Scan, m_maxScan);
}
var finder = new MSFeatureSingleLinkageClustering <MSFeatureLight, UMCLight>
{
Parameters =
{
DistanceFunction = WeightedNETDistanceFunction,
RangeFunction = WithinRange,
Tolerances = { Mass = options.ConstraintMonoMass, RetentionTime = 100, DriftTime = 100 }
}
};
finder.Parameters.CentroidRepresentation = centroidType;
m_maxDistance = options.MaxDistance;
features = finder.Cluster(rawMsFeatures);
// Remove the short UMC's.
features.RemoveAll(x => (x.ScanEnd - x.ScanStart + 1) < options.MinUMCLength);
var id = 0;
foreach (var feature in features)
{
feature.NET = Convert.ToDouble(feature.Scan - m_minScan) / Convert.ToDouble(m_maxScan - m_minScan);
feature.RetentionTime = feature.NET;
feature.ID = id++;
}
return(features);
}
/// <summary>
/// Finds LCMS Features using the PNNL Omics linkage clustering algorithms.
/// </summary>
public List<UMCLight> FindFeatures( List<MSFeatureLight> rawMsFeatures,
LCMSFeatureFindingOptions options,
ISpectraProvider provider)
{
const ClusterCentroidRepresentation centroidType = ClusterCentroidRepresentation.Mean;
List<UMCLight> features = null;
m_options = options;
m_minScan = int.MaxValue;
m_maxScan = int.MinValue;
foreach (var feature in rawMsFeatures)
{
m_minScan = Math.Min(feature.Scan, m_minScan);
m_maxScan = Math.Max(feature.Scan, m_maxScan);
}
var finder = new MSFeatureSingleLinkageClustering<MSFeatureLight, UMCLight>
{
Parameters =
{
DistanceFunction = WeightedNETDistanceFunction,
RangeFunction = WithinRange,
Tolerances = {Mass = options.ConstraintMonoMass, RetentionTime = 100, DriftTime = 100}
}
};
finder.Parameters.CentroidRepresentation = centroidType;
m_maxDistance = options.MaxDistance;
features = finder.Cluster(rawMsFeatures);
// Remove the short UMC's.
features.RemoveAll(x => (x.ScanEnd - x.ScanStart + 1) < options.MinUMCLength);
var id = 0;
foreach (var feature in features)
{
feature.NET = Convert.ToDouble(feature.Scan - m_minScan) / Convert.ToDouble(m_maxScan - m_minScan);
feature.RetentionTime = feature.NET;
feature.ID = id++;
}
return features;
}
