public void TestPromexClustering()
{
var provider = new ScanSummaryProviderCache();
var reader1 = provider.GetScanSummaryProvider(pbf1, 0) as InformedProteomicsReader;
var reader2 = provider.GetScanSummaryProvider(pbf2, 1) as InformedProteomicsReader;
var reader3 = provider.GetScanSummaryProvider(pbf3, 2) as InformedProteomicsReader;
var promexFileReader1 = new PromexFileReader(reader1, 0);
var features1 =
promexFileReader1.ReadFile(ms1ft1);
var promexFileReader2 = new PromexFileReader(reader2, 1);
var features2 =
promexFileReader2.ReadFile(ms1ft2);
var promexFileReader3 = new PromexFileReader(reader3, 2);
var features3 =
promexFileReader3.ReadFile(ms1ft3);
var features = new List <UMCLight>();
features.AddRange(features1);
features.AddRange(features2);
features.AddRange(features3);
var clusterer = new PromexClusterer
{
Readers = provider,
};
var clusters = clusterer.Cluster(features);
Console.WriteLine(clusters.Count(c => c.Features.Count > 1));
}
public void CompareClustering()
{
// Cluster using MultiAlign to Promex adapters
var provider = new ScanSummaryProviderCache();
var reader1 = provider.GetScanSummaryProvider(pbf1, 0) as InformedProteomicsReader;
var reader2 = provider.GetScanSummaryProvider(pbf2, 1) as InformedProteomicsReader;
var promexFileReader1 = new PromexFileReader(reader1, 0);
var features1 = promexFileReader1.ReadFile(ms1ft1);
var promexFileReader2 = new PromexFileReader(reader2, 1);
var features2 =
promexFileReader2.ReadFile(ms1ft2);
var features = new List <UMCLight>();
features.AddRange(features1);
features.AddRange(features2);
var clusterer = new PromexClusterer
{
Readers = provider,
};
var clusters = clusterer.Cluster(features);
var clusterCount = clusters.Count(c => c.UmcList.Count > 1);
// Cluster using only ProMex
var lcmsRun1 = PbfLcMsRun.GetLcMsRun(pbf1);
var lcmsRun2 = PbfLcMsRun.GetLcMsRun(pbf2);
var aligner = new LcMsFeatureAlignment(new LcMsFeatureAlignComparer(new Tolerance(10, ToleranceUnit.Ppm)));
var promexFeatures1 = LcMsFeatureAlignment.LoadProMexResult(0, ms1ft1, lcmsRun1);
aligner.AddDataSet(0, promexFeatures1, lcmsRun1);
var promexFeatures2 = LcMsFeatureAlignment.LoadProMexResult(1, ms1ft2, lcmsRun2);
aligner.AddDataSet(1, promexFeatures2, lcmsRun2);
aligner.AlignFeatures();
var promexClusters = aligner.GetAlignedFeatures();
var promexClusterCount = promexClusters.Count(c => c.Count(f => f != null) > 1);
Assert.AreEqual(clusters.Count, promexClusters.Count);
Assert.AreEqual(clusterCount, promexClusterCount);
}
