/// <summary>
/// Calculates pairwise distances between features in the list of
/// potential features to cluster.
/// </summary>
/// <param name="start">Start UMC index.</param>
/// <param name="stop">Stop UMC index.</param>
/// <param name="data">List of data to compute distances over.</param>
/// <returns>List of UMC distances to consider during clustering.</returns>
protected virtual List <Data.PairwiseDistance <T> > CalculatePairWiseDistances(int start, int stop, List <T> data)
{
var massTolerance = Parameters.Tolerances.Mass;
var netTolerance = Parameters.Tolerances.Net;
var driftTolerance = Parameters.Tolerances.DriftTime;
var onlyClusterSameChargeStates = Parameters.OnlyClusterSameChargeStates;
var distances = new List <Data.PairwiseDistance <T> >();
for (var i = start; i < stop; i++)
{
var featureX = data[i];
var driftTimeX = featureX.DriftTime;
var netAlignedX = featureX.Net;
var massAlignedX = featureX.MassMonoisotopicAligned;
var chargeStateX = featureX.ChargeState;
for (var j = i + 1; j <= stop; j++)
{
// Don't calculate distance to self.
var featureY = data[j];
// Calculate the distances here (using a cube). We dont care if we are going to re-compute
// these again later, because here we want to fall within the cube, the distance function used
// later is more related to determining a scalar value instead.
var withinRange = AreClustersWithinTolerance(featureX, featureY); //Parameters.RangeFunction(featureX, featureY);
// Make sure we fall within the distance range before computing...
if (withinRange)
{
// If IMS or equivalent only cluster similar charge states
if (onlyClusterSameChargeStates)
{
// Make sure it's the same charge state
if (chargeStateX == featureY.ChargeState)
{
// Calculate the pairwise distance
var pairwiseDistance = new Data.PairwiseDistance <T>();
pairwiseDistance.FeatureX = featureX;
pairwiseDistance.FeatureY = featureY;
pairwiseDistance.Distance = Parameters.DistanceFunction(featureX, featureY);
distances.Add(pairwiseDistance);
}
}
else
{
// Calculate the pairwise distance
var pairwiseDistance = new Data.PairwiseDistance <T>();
pairwiseDistance.FeatureX = featureX;
pairwiseDistance.FeatureY = featureY;
pairwiseDistance.Distance = Parameters.DistanceFunction(featureX, featureY);
distances.Add(pairwiseDistance);
}
}
}
}
return(distances);
}
/// <summary>
/// Calculates pairwise distances between features in the list of
/// potential features to cluster.
/// </summary>
/// <param name="start">Start UMC index.</param>
/// <param name="stop">Stop UMC index.</param>
/// <param name="data">List of data to compute distances over.</param>
/// <returns>List of UMC distances to consider during clustering.</returns>
protected List <Data.PairwiseDistance <U> > CalculateDistances(Dictionary <int, U> clusters)
{
var massTolerance = Parameters.Tolerances.Mass;
var netTolerance = Parameters.Tolerances.Net;
var driftTolerance = Parameters.Tolerances.DriftTime;
var onlyClusterSameChargeStates = Parameters.OnlyClusterSameChargeStates;
var distances = new List <Data.PairwiseDistance <U> >();
foreach (var clusterI in clusters.Values)
{
var driftTimeX = clusterI.DriftTime;
var netAlignedX = clusterI.Net;
var massAlignedX = clusterI.MassMonoisotopicAligned;
var chargeStateX = clusterI.ChargeState;
foreach (var clusterJ in clusters.Values)
{
// Don't calculate distance to other features within same group
if (clusterI == clusterJ)
{
continue;
}
// Calculate the distances here (using a cube). We dont care if we are going to re-compute
// these again later, because here we want to fall within the cube, the distance function used
// later is more related to determining a scalar value instead.
var massDiff = Math.Abs(FeatureLight.ComputeMassPPMDifference(massAlignedX,
clusterJ.MassMonoisotopicAligned));
var netDiff = Math.Abs(netAlignedX - clusterJ.Net);
var driftDiff = Math.Abs(driftTimeX - clusterJ.DriftTime);
// Make sure we fall within the distance range before computing...
if (massDiff <= massTolerance && netDiff <= netTolerance && driftDiff <= driftTolerance)
{
// If IMS or equivalent only cluster similar charge states
if (onlyClusterSameChargeStates)
{
// Make sure it's the same charge state
if (chargeStateX == clusterJ.ChargeState)
{
// Calculate the pairwise distance
var pairwiseDistance = new Data.PairwiseDistance <U>();
pairwiseDistance.FeatureX = clusterI;
pairwiseDistance.FeatureY = clusterJ;
pairwiseDistance.Distance = GetAverageClusterDistance(clusterI, clusterJ, Parameters.DistanceFunction);
distances.Add(pairwiseDistance);
}
}
else
{
// Calculate the pairwise distance
var pairwiseDistance = new Data.PairwiseDistance <U>();
pairwiseDistance.FeatureX = clusterI;
pairwiseDistance.FeatureY = clusterJ;
pairwiseDistance.Distance = GetAverageClusterDistance(clusterI, clusterJ, Parameters.DistanceFunction);
distances.Add(pairwiseDistance);
}
}
}
}
return(distances);
}
