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); }