public static List <ProteinSpectrumMatchSet> GroupingByPrsm(int dataid, IEnumerable <ProteinSpectrumMatch> matches, INodeComparer <ProteinSpectrumMatch> prsmComparer)
{
var prsmSet = new NodeSet <ProteinSpectrumMatch>()
{
};
prsmSet.AddRange(matches);
var groupList = prsmSet.ConnnectedComponents(prsmComparer);
return(groupList.Select(@group => new ProteinSpectrumMatchSet(dataid, @group)).ToList());
}
public ProteinSpectrumMatchSet[][] GroupAcrossRuns(List <ProteinSpectrumMatchSet>[] prsmGroup, INodeComparer <ProteinSpectrumMatchSet> prsmGroupComparer)
{
var nDataset = prsmGroup.Length;
var prsmSet = new NodeSet <ProteinSpectrumMatchSet>()
{
};
for (var i = 0; i < nDataset; i++)
{
var groupedPrsms = prsmGroup[i];
if (groupedPrsms == null)
{
continue;
}
prsmSet.AddRange(groupedPrsms);
}
var alignedPrsms = prsmSet.ConnnectedComponents(prsmGroupComparer);
var alignedResult = new ProteinSpectrumMatchSet[alignedPrsms.Count][];
for (var i = 0; i < alignedResult.Length; i++)
{
alignedResult[i] = new ProteinSpectrumMatchSet[nDataset];
}
for (var i = 0; i < alignedPrsms.Count; i++)
{
foreach (var set in alignedPrsms[i])
{
if (alignedResult[i][set.DataId] != null)
{
alignedResult[i][set.DataId].Merge(set);
//Console.WriteLine("[{4}] {0}-{1}...{2}-{3}", set.MinScanNum, set.MaxScanNum, alignedResult[i][set.DataId].MinScanNum, alignedResult[i][set.DataId].MaxScanNum, set.DataId);
}
else
{
alignedResult[i][set.DataId] = set;
}
}
}
return(alignedResult);
}
private List <LcMsPeakCluster> MergeFeatures(LcMsPeakMatrix featureFinder, List <LcMsPeakCluster> features)
{
//foreach (var f in _featureList) f.ActivateAllPeaks();
var featureSet = new NodeSet <LcMsPeakCluster>();
featureSet.AddRange(features);
var connectedFeatureSet = featureSet.ConnnectedComponents(_mergeComparer);
var mergedFeatures = new List <LcMsPeakCluster>();
foreach (var fSet in connectedFeatureSet)
{
if (fSet.Count == 1)
{
mergedFeatures.Add(fSet[0]);
}
else
{
var maxScan = fSet.Max(f => f.MaxScanNum);
var minScan = fSet.Min(f => f.MinScanNum);
var maxCharge = fSet.Max(f => f.MaxCharge);
var minCharge = fSet.Min(f => f.MinCharge);
var maxScore = double.MinValue;//fSet.Max(f => f.Score);
LcMsPeakCluster maxScoredClusterOriginal = null;
LcMsPeakCluster maxScoredCluster = null;
foreach (var f in fSet)
{
var newFeature = featureFinder.GetLcMsPeakCluster(f.RepresentativeMass, minCharge, maxCharge, minScan, maxScan);
if (newFeature != null && (maxScoredCluster == null || newFeature.Score > maxScoredCluster.Score))
{
maxScoredCluster = newFeature;
}
if (f.Score > maxScore)
{
maxScoredClusterOriginal = f;
maxScore = f.Score;
}
}
var feature = featureFinder.GetLcMsPeakCluster(fSet.Select(f => f.Mass).Mean(), minCharge, maxCharge, minScan, maxScan);
if (feature != null && (maxScoredCluster == null || feature.Score > maxScoredCluster.Score))
{
maxScoredCluster = feature;
}
//Console.WriteLine("------------- Merge -----------------");
//foreach (var f in fSet) Console.WriteLine("*\t{0}\t{1}\t{2}\t{3}", f.RepresentativeMass, f.MinScanNum, f.MaxScanNum, f.Score);
//Console.WriteLine("**\t{0}\t{1}\t{2}\t{3}", maxScoredCluster.RepresentativeMass, maxScoredCluster.MinScanNum, maxScoredCluster.MaxScanNum, maxScoredCluster.Score);
if (maxScoredCluster == null)
{
maxScoredCluster = maxScoredClusterOriginal;
}
if (maxScoredCluster.Score < maxScore)
{
maxScoredCluster.Score = maxScore;
}
mergedFeatures.Add(maxScoredCluster);
}
//if (selectedFeature != null) postFilteredSet.Add(selectedFeature);
}
//return postFilteredSet.OrderBy(f => f.RepresentativeMass);
return(mergedFeatures);
}
