public void TestUmcFeatures(string path)
{
var reader = new MSFeatureLightFileReader {
Delimeter = ","
};
var newMsFeatures = reader.ReadFile(path);
var finder = new UMCFeatureFinder();
var options = new LCMSFeatureFindingOptions
{
AveMassWeight = .01f,
ConstraintAveMass = 6,
ConstraintMonoMass = 6,
FitWeight = .1f,
IsIsotopicFitFilterInverted = false,
IsotopicFitFilter = .15,
IsotopicIntensityFilter = 0,
LogAbundanceWeight = .1f,
MaxDistance = .1,
MinUMCLength = 3,
MonoMassWeight = .01f,
NETWeight = .1f,
ScanWeight = .01f,
UMCAbundanceReportingType = AbundanceReportingType.Max,
UseIsotopicFitFilter = true,
UseIsotopicIntensityFilter = false,
UseNET = true
};
var start = DateTime.Now;
var umcs = finder.FindFeatures(newMsFeatures.ToList(), options, null);
var end = DateTime.Now;
Console.WriteLine(end.Subtract(start).TotalSeconds);
Assert.Greater(umcs.Count, 0);
}
/// <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);
}
