public void Execute(Run run)
{
Check.Require(run != null, "'Run' has not be defined");
Check.Require(run.Filename != null &&
run.Filename.Length > 0, "MS data file ('run') has not been initialized");
//Check.Require(run.ScanSetCollection != null && run.ScanSetCollection.ScanSetList.Count > 0, "ChromAligner failed. ScanSets have not been defined.");
if (m_targetUMCFileStoringAlignmentInfo == null)
{
var baseFileName = Path.Combine(run.DataSetPath, run.DatasetName);
m_targetUMCFileStoringAlignmentInfo = baseFileName + "_UMCs.txt";
}
Check.Require(File.Exists(m_targetUMCFileStoringAlignmentInfo), "ChromAligner failed. The UMC file from which alignment data is extracted does not exist.");
var umcs = new UMCCollection();
var importer = new UMCFileImporter(m_targetUMCFileStoringAlignmentInfo, '\t');
umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
run.NetAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
run.NetAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
}
public void importUMCsWithO16O18PairedDataTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
Assert.AreEqual(23073, umcs.UMCList.Count);
}
public void importUMCsTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcTestfile1, '\t');
importer.Import(umcs);
Assert.AreEqual(15381, umcs.UMCList.Count);
}
public void filterUMCsByMassTagsTest2()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
UMCCollection filteredUMCs = new UMCCollection();
filteredUMCs.UMCList = umcs.FilterUMCsByMassTagMatch(new List <int> {
22807265, 22580887, 20791942, 20791939, 20750857, 20908613, 20842966, 22598396, 174124103
});
Assert.AreEqual(8, filteredUMCs.UMCList.Count);
filteredUMCs.DisplayUMCExpressionInfo();
}
public void filterOutPairedUMCsTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
UMCCollection filteredUMCs = new UMCCollection();
filteredUMCs.UMCList = umcs.FilterOutPairedData();
Assert.AreEqual(1734, filteredUMCs.UMCList.Count);
filteredUMCs.DisplayUMCExpressionInfo();
}
public void umcTest2()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcTestfile1, '\t');
importer.Import(umcs);
Stopwatch sw = new Stopwatch();
sw.Start();
Dictionary <int, double> lookupTable = umcs.GetScanNETLookupTable();
sw.Stop();
double netVal = lookupTable[6005];
netVal = lookupTable[6004];
Console.Write(sw.ElapsedMilliseconds);
Assert.AreEqual(0.3216, netVal);
}
