public void createTextFileRunTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(textFile1);
Assert.AreEqual(Globals.MSFileType.Ascii, run.MSFileType);
}
public void createIMSScanSets2()
{
var factory = new RunFactory();
var run = (UIMFRun)factory.CreateRun(FileRefs.RawDataMSFiles.UIMFStdFile3);
var numScansSummed = 7;
run.IMSScanSetCollection.Create(run, numScansSummed, 1);
Assert.IsNotNull(run.IMSScanSetCollection);
//tests the lowest ims_scans
Assert.AreEqual(360, run.IMSScanSetCollection.ScanSetList.Count);
Assert.AreEqual(4, run.IMSScanSetCollection.ScanSetList[0].IndexValues.Count);
Assert.AreEqual(0, run.IMSScanSetCollection.ScanSetList[0].IndexValues[0]);
Assert.AreEqual(3, run.IMSScanSetCollection.ScanSetList[0].IndexValues[3]);
var testIMSScan2 = 100;
Assert.AreEqual(7, run.IMSScanSetCollection.ScanSetList[testIMSScan2].IndexValues.Count);
Assert.AreEqual(100, run.IMSScanSetCollection.ScanSetList[testIMSScan2].IndexValues[3]);
Assert.AreEqual(100, run.IMSScanSetCollection.ScanSetList[testIMSScan2].PrimaryScanNumber);
}
public void UIMFTest1()
{
var uimffile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var rf = new RunFactory();
var run = rf.CreateRun(uimffile);
var expectedPeaksFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_peaks.txt";
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 500;
parameters.LCScanMax = 510;
parameters.NumIMSScansSummed = -1;
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedPeaksFile));
}
public void createAgilentDRunTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.AgilentDFile1);
Assert.AreEqual(Globals.MSFileType.Agilent_D, run.MSFileType);
}
public void Import_NET_And_MassAlignment_Test1()
{
string mzAlignmentInfoFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
string NETAlignmentInfoFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
MassAlignmentInfoFromTextImporter importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
run.AlignmentInfo = importer.Import();
NETAlignmentFromTextImporter netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
netAlignmentInfoImporter.ImportIntoAlignmentInfo(run.AlignmentInfo); //this will append the NET alignment info to the AlignmentInfo object
float testScan = 6439;
float testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
float ppmshift = run.AlignmentInfo.GetPPMShiftFromTimeMZ(testScan, testMZ);
Console.WriteLine("ppm shift = " + ppmshift);
float testScan2 = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan2);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
public void creatorTest_ensureOnlyMS1_test1()
{
//note that frame 26 is a calibration frame. So we don't want to have this if we are summing frames
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.UIMFStdFile4); //Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf
var frameStart = 24;
var frameStop = 28;
var numFramesToSum = 3;
var uimfRun = (UIMFRun)run;
uimfRun.ScanSetCollection.Create(uimfRun, frameStart, frameStop, numFramesToSum, 1);
Assert.AreEqual(4, uimfRun.ScanSetCollection.ScanSetList.Count);
Assert.AreEqual("25 {24, 25, 27}", uimfRun.ScanSetCollection.ScanSetList[1].ToString());
//FrameSet testFrame0 = uimfRun.ScanSetCollection.ScanSetList[1];
//Assert.AreEqual(3, testFrame0.IndexValues.Count);
//Assert.AreEqual(1, testFrame0.IndexValues[0]);
}
public void createRunAndReadMSSpectraTest1()
{
//Create the run
var runFactory = new RunFactory();
var run = runFactory.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//Create the task
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
//Create the target scan list (MS1 scans from 6005 - 6020).
run.ScanSetCollection.Create(run, 6005, 6020, 1, 1);
//iterate over each scan in the target collection get the mass spectrum
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
Console.WriteLine("Working on Scan " + scan.PrimaryScanNumber);
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
Console.WriteLine("XYPair count = " + run.XYData.Xvalues.Length);
}
}
public void Import_NET_And_MassAlignment_Test1()
{
var mzAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var NETAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
float testScan = 6439;
var testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(testMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
var testScan2 = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan(testScan2);
Assert.AreEqual(0.3252918m, (decimal)Math.Round(testNET1, 7));
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
public void checkRetrievalOfScanValueForAGivenNET()
{
var NETAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
var testNET1 = 0.95f;
var testNET2 = 0.08f;
var scan1 = (int)run.NetAlignmentInfo.GetScanForNet(testNET1);
var scan2 = (int)run.NetAlignmentInfo.GetScanForNet(testNET2);
Assert.AreEqual(18231, scan1);
Assert.AreEqual(1113, scan2);
//foreach (var item in scanNETdata)
//{
// Console.WriteLine(item);
//}
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine(scan1 + " was returned for NET= " + testNET1);
}
public void getMSMSDataTest1()
{
//Create the run
var runFactory = new RunFactory();
var run = runFactory.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//Create the task
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakdetector = new DeconToolsPeakDetectorV2();
var startScan = 6000;
var stopScan = 7000;
for (var i = startScan; i < stopScan; i++)
{
if (run.GetMSLevel(i) == 2)
{
var scanset = new ScanSet(i);
run.CurrentScanSet = scanset;
msgen.Execute(run.ResultCollection);
peakdetector.Execute(run.ResultCollection);
Console.Write("Working on Scan " + scanset.PrimaryScanNumber);
Console.WriteLine("; XYPair count = " + run.XYData.Xvalues.Length);
Console.WriteLine("num peaks= " + run.PeakList.Count);
}
}
}
public void ImportMassAndTimePPMCorrections_and_Try_Alignment_Test1()
{
var importFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(importFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
float testScan = 6439;
var testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(testMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
public void creator_endFramesTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.UIMFStdFile3);
var frameStop = ((UIMFRun)run).MaxLCScan;
var frameStart = frameStop - 10;
var uimfrun = (UIMFRun)run;
uimfrun.ScanSetCollection.Create(uimfrun, frameStart, frameStop, 3, 1);
Assert.AreEqual(11, uimfrun.ScanSetCollection.ScanSetList.Count);
foreach (var frameset in uimfrun.ScanSetCollection.ScanSetList)
{
Console.WriteLine(frameset);
}
var testFrame0 = uimfrun.ScanSetCollection.ScanSetList[0];
Assert.AreEqual(3, testFrame0.IndexValues.Count);
Assert.AreEqual(1164, testFrame0.IndexValues[0]);
Assert.AreEqual(1165, testFrame0.IndexValues[1]);
Assert.AreEqual(1166, testFrame0.IndexValues[2]);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void doAlignmentTest1()
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
Assert.IsNotNull(run.AlignmentInfo);
Assert.IsNotNull(run.AlignmentInfo.marrNETFncTimeInput);
Assert.AreEqual(2273.0f, run.AlignmentInfo.marrNETFncTimeInput[0]);
float testScan = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
string exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
string exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
NETAlignmentInfoToTextExporter exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
MassAlignmentInfoToTextExporter massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void creatorTest_sum7_test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.UIMFStdFile3);
var frameStart = 1;
var frameStop = 11;
var numFramesToSum = 7;
var uimfRun = (UIMFRun)run;
uimfRun.ScanSetCollection.Create(uimfRun, frameStart, frameStop, numFramesToSum, 1);
Assert.AreEqual(11, uimfRun.ScanSetCollection.ScanSetList.Count);
foreach (var frameset in uimfRun.ScanSetCollection.ScanSetList)
{
Console.WriteLine(frameset);
}
var testFrame0 = uimfRun.ScanSetCollection.ScanSetList[3];
Assert.AreEqual(1, testFrame0.IndexValues.First());
Assert.AreEqual(7, testFrame0.IndexValues.Count);
Assert.AreEqual(7, testFrame0.IndexValues.Last());
}
public void agilentDeconTest1()
{
RunFactory runFact = new RunFactory();
Run run = runFact.CreateRun(agilentFile);
MSGeneratorFactory msfactory = new MSGeneratorFactory();
Task msgen = msfactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 7;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
ScanSet scan1821 = new ScanSet(1821);
run.CurrentScanSet = scan1821;
msgen.Execute(run.ResultCollection);
run.XYData = run.XYData.TrimData(450, 520, TODO);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void peakexporterTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 5500;
parameters.LCScanMax = 6500;
parameters.OutputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TempOutput";
var expectedPeaksFile = Path.Combine(parameters.OutputFolder, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
var fileinfo = new FileInfo(expectedPeaksFile);
Assert.IsTrue(fileinfo.Exists);
Assert.IsTrue(fileinfo.Length > 1000000);
}
public static Run CreateAndAlignRun(string fileOrDirectoryPath, string peaksFile)
{
var directoryExists = Directory.Exists(fileOrDirectoryPath);
var fileExists = File.Exists(fileOrDirectoryPath);
Check.Require(directoryExists || fileExists, "Dataset file (or directory) not found error when RunUtilities tried to create Run.");
var rf = new RunFactory();
var run = rf.CreateRun(fileOrDirectoryPath);
Check.Ensure(run != null, "RunUtilities could not create run. Run is null.");
//Console.WriteLine(run.DatasetName + " loaded.");
AlignRunUsingAlignmentInfoInFiles(run);
string sourcePeaksFile;
if (string.IsNullOrEmpty(peaksFile))
{
// ReSharper disable once PossibleNullReferenceException (already checked for null above)
sourcePeaksFile = Path.Combine(run.DatasetDirectoryPath, run.DatasetName + "_peaks.txt");
}
else
{
sourcePeaksFile = peaksFile;
}
GetPeaks(run, sourcePeaksFile);
// Console.WriteLine("Peaks loaded = " + run.ResultCollection.MSPeakResultList.Count);
return(run);
}
public void doAlignmentTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
float testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan((int)testScan);
//note - this is Multialign's
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void UnknownDatasetTypeTest1()
{
var testfile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Other_testFileTypes\sampleXYData.wiffer";
var rf = new RunFactory();
var run = rf.CreateRun(testfile);
}
public void createBruker_fromBruker9T_Test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.Bruker9TStandardFile1);
Assert.AreEqual(Globals.MSFileType.Bruker, run.MSFileType);
Assert.AreEqual(599, run.MaxLCScan);
}
public void createBrukerSolarixRunTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.BrukerSolarix12TFile1);
Assert.AreEqual(Globals.MSFileType.Bruker, run.MSFileType);
Assert.AreEqual(7, run.MaxLCScan);
}
public void createBruker_fromBruker12T_FID_Test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.BrukerSolarix12T_FID_File1);
Assert.IsNotNull(run);
Assert.AreEqual(Globals.MSFileType.Bruker, run.MSFileType);
Assert.AreEqual(0, run.MaxLCScan);
}
public void Test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var ssf = new ScanSetFactory();
var scan = ssf.CreateScanSet(run, 6005, 11);
Console.WriteLine(scan);
}
public void oldSchoolTest1()
{
string testFile = @"D:\Data\UIMF\Problem_datasets\FPGA\QCSHEW_FPGA_99min_0003.UIMF";
string paramFile = @"D:\Data\UIMF\Problem_datasets\FPGA\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScansAll_SumFrames3_RAPID_2011-02-09_temp.xml";
RunFactory rf = new RunFactory();
UIMFRun run = (UIMFRun)rf.CreateRun(testFile);
//OldSchoolProcRunner proc = new OldSchoolProcRunner(testFile, run.MSFileType, paramFile);
//proc.Execute();
}
public void CreateMZ5RunTest1()
{
var testfile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\mzXML\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.mz5";
var rf = new RunFactory();
var run = rf.CreateRun(testfile);
Assert.AreEqual(Globals.MSFileType.MZ5, run.MSFileType);
Assert.AreEqual(18504, run.MaxLCScan);
}
public void CreateSingleScansetThatSumsAll()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, true, true);
Console.WriteLine(run.ScanSetCollection.ScanSetList[0]);
Assert.AreEqual(2695, run.ScanSetCollection.ScanSetList[0].IndexValues.Count);
}
public void CreateBrukerTOFRunTest1()
{
var testfile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Bruker\Bruker_Maxis\2012_05_15_MN9_A_000001.d";
var rf = new RunFactory();
var run = rf.CreateRun(testfile);
Assert.AreEqual(Globals.MSFileType.Bruker, run.MSFileType);
Assert.IsTrue(run is BrukerTOF);
Assert.AreEqual(1131, run.GetNumMSScans());
}
public void CreateScanSetBasedOnRangeOfScansTest1()
{
var startScan = 5970;
var stopScan = 6035;
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var ssf = new ScanSetFactory();
var scan = ssf.CreateScanSet(run, 6005, startScan, stopScan);
Assert.AreEqual("6005 {5970, 5977, 5984, 5991, 5998, 6005, 6012, 6019, 6026, 6033}", scan.ToString());
}
private void InitializeRun(string datasetName)
{
//Datasets have to all be in the same folder
//currently works for datasets that have a File reference as
//opposed to datasets having a Folder reference (Agilent/Bruker)
DirectoryInfo dirInfo = new DirectoryInfo(_fileInputs.DatasetDirectory);
var fileInfo = dirInfo.GetFiles(datasetName + ".*");
if (!fileInfo.Any())
{
throw new FileNotFoundException("Run could not be initialized. File not found");
}
RunFactory rf = new RunFactory();
Run = rf.CreateRun(fileInfo.First().FullName);
bool peaksFileExists = checkForPeaksFile();
if (!peaksFileExists)
{
ReportGeneralProgress("Creating extracted ion chromatogram (XIC) source data... takes 1-5 minutes.. only needs to be done once.");
CreatePeaksForChromSourceData();
ReportGeneralProgress("Done creating XIC source data.");
}
string baseFileName;
baseFileName = this.Run.DataSetPath + "\\" + this.Run.DatasetName;
string expectedPeaksFilename = baseFileName + "_peaks.txt";
if (File.Exists(expectedPeaksFilename))
{
PeakImporterFromText peakImporter = new PeakImporterFromText(expectedPeaksFilename, _backgroundWorker);
peakImporter.ImportPeaks(this.Run.ResultCollection.MSPeakResultList);
}
else
{
ReportGeneralProgress(DateTime.Now + "\tCRITICAL FAILURE. Chrom source data (_peaks.txt) file not loaded.");
return;
}
ReportGeneralProgress(DateTime.Now + "\tPeak Loading complete.");
return;
}
