public void WatersMzXmlTest1()
{
var testfile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Waters\LC_MS_pHis_Caulo_meth_110207.mzXML";
var run = new RunFactory().CreateRun(testfile);
Console.WriteLine(TestUtilities.DisplayRunInformation(run));
run.ScanSetCollection = new ScanSetCollection();
run.ScanSetCollection.Create(run, 500, 600, 1, 1);
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
var level = run.GetMSLevel(scanSet.PrimaryScanNumber);
Console.WriteLine(scanSet + "\t" + level);
}
}
public void msgenTest1()
{
var run = new RunFactory().CreateRun(_testdatafile);
var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
ScanSet scan = new ScanSet(1);
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
Console.WriteLine("scan\tmsLevel");
for (int i = run.MinLCScan; i < run.MaxLCScan; i++)
{
Console.WriteLine(i + "\t" + run.GetMSLevel(i));
}
//TestUtilities.DisplayXYValues(run.XYData);
}
public void Test1()
{
var run =
new RunFactory().CreateRun(
@"\\proto-7\VOrbiETD01\2012_3\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08.raw");
Assert.IsNotNull(run);
var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentScanSet = new ScanSet(20000);
run.ScanSetCollection.Create(run, 3000, 3010, 1, 1, true);
Console.WriteLine("scan\tz\tinfo");
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanSet;
msGen.Execute(run.ResultCollection);
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + run.GetMSLevel(scanSet.PrimaryScanNumber) + "\t" + run.GetScanInfo(scanSet.PrimaryScanNumber));
}
}
public void Test1()
{
var run =
new RunFactory().CreateRun(
@"D:\Data\From_Joe\MyDeconToolsTester\RawFiles\Transition_Selection_Orbitrap_HCD_8Mar13_Cougar_12-12-36.raw");
Assert.IsNotNull(run);
var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
int testScan = 2448;
run.CurrentScanSet = new ScanSet(testScan);
DeconToolsPeakDetectorV2 ms1PeakDetector = new DeconToolsPeakDetectorV2();
ms1PeakDetector.PeakToBackgroundRatio = 1.3;
ms1PeakDetector.SignalToNoiseThreshold = 2;
ms1PeakDetector.IsDataThresholded = true;
DeconToolsPeakDetectorV2 ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2();
DeconToolsPeakDetectorV2 ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2();
ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2();
ms2PeakDetectorForProfileData.PeakToBackgroundRatio = ms1PeakDetector.PeakToBackgroundRatio;
ms2PeakDetectorForProfileData.SignalToNoiseThreshold = ms1PeakDetector.SignalToNoiseThreshold;
ms2PeakDetectorForProfileData.IsDataThresholded = ms1PeakDetector.IsDataThresholded;
ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true);
ms2PeakDetectorForCentroidedData.RawDataType = Globals.RawDataType.Centroided;
run.ScanSetCollection.Create(run, testScan, testScan, 1, 1, true);
Console.WriteLine("scan\tz\tinfo");
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
if (run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
ms1PeakDetector.Execute(run.ResultCollection);
}
else
{
var dataIsCentroided = run.IsDataCentroided(scan.PrimaryScanNumber);
Console.WriteLine("Scan " + scan.PrimaryScanNumber + "centroided=" + dataIsCentroided);
TestUtilities.DisplayXYValues(run.XYData);
if (dataIsCentroided)
{
ms2PeakDetectorForCentroidedData.Execute(run.ResultCollection);
}
else
{
ms2PeakDetectorForProfileData.Execute(run.ResultCollection);
}
}
Console.WriteLine("---- peaks for Scan " + scan);
TestUtilities.DisplayPeaks(run.PeakList);
}
}
public void ChromAnalysisForAllSelectedPrecursors()
{
var isDataSmoothed = true;
var numPointsInSmoothing = 9;
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(numPointsInSmoothing, 2);
var graphGenerator = new BasicGraphControl();
var thermoFile1 = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(thermoFile1);
var outputFolderForChromGraphs = @"\\protoapps\DataPkgs\Public\2012\684_DeconMSn_research1\ChromatogramImages";
if (!Directory.Exists(outputFolderForChromGraphs))
{
Directory.CreateDirectory(outputFolderForChromGraphs);
}
var scanSetCollection = new ScanSetCollection();
var scanStart = run.MinLCScan;
var scanStop = run.MaxLCScan;
scanSetCollection.Create(run, scanStart, scanStop, 1, 1, true);
var sb = new StringBuilder();
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (!File.Exists(expectedPeaksFile))
{
var peakCreatorParams = new PeakDetectAndExportWorkflowParameters();
peakCreatorParams.PeakBR = 1.75;
var peakCreator = new PeakDetectAndExportWorkflow(run, peakCreatorParams);
peakCreator.Execute();
}
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
double ppmTol = 50;
var peakChromatogramGenerator = new PeakChromatogramGenerator(ppmTol, Globals.ChromatogramGeneratorMode.MZ_BASED);
var scansetList = scanSetCollection.ScanSetList;
var scanCounter = 0;
var currentBin = 0;
foreach (var scanSet in scansetList)
{
run.CurrentScanSet = scanSet;
var currentScanLevel = run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentScanLevel > 1)
{
scanCounter++;
var precursorInfo = run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
var scanInfo = run.GetScanInfo(scanSet.PrimaryScanNumber);
var scanWindowSize = 400;
var startScan = scanSet.PrimaryScanNumber - scanWindowSize / 2;
var stopScan = scanSet.PrimaryScanNumber + scanWindowSize / 2;
run.XYData = peakChromatogramGenerator.GenerateChromatogram(run, startScan, stopScan, precursorInfo.PrecursorMZ, ppmTol);
if (run.XYData == null)
{
run.XYData = new XYData();
run.XYData.Xvalues = new double[] { 0, 1, 2 };
run.XYData.Yvalues = new double[] { 0, 1, 2 };
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan + "--------- NO XYData!!! -------------");
}
else
{
if (isDataSmoothed)
{
run.XYData = smoother.Smooth(run.XYData);
}
}
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan);
graphGenerator.GenerateGraph(run.XYData.Xvalues, run.XYData.Yvalues);
var line = graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 2;
line.Symbol.Type = SymbolType.Circle;
graphGenerator.GraphPane.XAxis.Title.Text = "scan";
graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
graphGenerator.GraphPane.XAxis.Scale.MinAuto = true;
graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
graphGenerator.GraphPane.YAxis.Scale.Min = 0;
graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
graphGenerator.AddVerticalLineToGraph(scanSet.PrimaryScanNumber, 3);
graphGenerator.AddAnnotationRelativeAxis(scanInfo, 0.3, 0.1);
if (scanCounter > 500)
{
currentBin++;
scanCounter = 0;
}
var currentOutputFolder = Path.Combine(outputFolderForChromGraphs, "bin" + currentBin);
if (!Directory.Exists(currentOutputFolder))
{
Directory.CreateDirectory(currentOutputFolder);
}
var baseFilename = Path.Combine(currentOutputFolder,
scanSet.PrimaryScanNumber.ToString().PadLeft(5, '0') + "_mz" + precursorInfo.PrecursorMZ);
string outputGraphFilename;
string outputXYData;
if (isDataSmoothed)
{
outputGraphFilename = baseFilename + "_smoothed_chrom.png";
outputXYData = baseFilename + "_smoothed_xydata.txt";
}
else
{
outputXYData = baseFilename + "_xydata.txt";
outputGraphFilename = baseFilename + "_chrom.png";
}
graphGenerator.SaveGraph(outputGraphFilename);
TestUtilities.WriteToFile(run.XYData, outputXYData);
}
}
Console.WriteLine(sb.ToString());
}