public static IPeakListExporter Create(Globals.ExporterType exporterType, Globals.MSFileType fileType, int triggerValue, string outputFileName)
{
IPeakListExporter exporter;
switch (exporterType)
{
case Globals.ExporterType.Text:
exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName);
break;
case Globals.ExporterType.Sqlite:
exporter = new PeakListSQLiteExporter(triggerValue, outputFileName);
break;
default:
exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName);
break;
}
return(exporter);
}
public void ExportPeakDataToTextFileTest1()
{
var outputFile = FileRefs.OutputFolderPath + "ExportPeakDataToTextFileTest1.txt";
if (File.Exists(outputFile))
{
File.Delete(outputFile);
}
var run = TestDataCreationUtilities.CreatePeakDataFromStandardOrbitrapData();
NUnit.Framework.Assume.That(5608 == run.ResultCollection.MSPeakResultList.Count);
var peakExporter = new PeakListTextExporter(run.MSFileType, outputFile);
peakExporter.WriteOutPeaks(run.ResultCollection.MSPeakResultList);
var fi = new FileInfo(outputFile);
Assert.AreEqual(true, fi.Exists);
Assert.AreNotEqual(0, fi.Length);
}
public void Execute()
{
InitializeWorkflow();
if (Run.MSFileType == Globals.MSFileType.PNNL_UIMF)
{
IMSScanSetCollection = CreateIMSScanSetCollection();
}
LcScanSetCollection = CreateLcScanSetCollection();
PrepareOutputDirectory(WorkflowParameters.OutputDirectory);
var outputPeaksFilePath = getOutputPeaksFilename();
peakExporter = new PeakListTextExporter(Run.MSFileType, outputPeaksFilePath);
var numTotalScans = LcScanSetCollection.ScanSetList.Count;
var lastProgress = DateTime.UtcNow;
using (var sw = new StreamWriter(new FileStream(outputPeaksFilePath, FileMode.Append, FileAccess.Write, FileShare.Read)))
{
if (Run.MSFileType == Globals.MSFileType.PNNL_UIMF && Run is UIMFRun uimfRun)
{
var numTotalFrames = LcScanSetCollection.ScanSetList.Count;
var frameCounter = 0;
foreach (var frameSet in LcScanSetCollection.ScanSetList)
{
frameCounter++;
uimfRun.CurrentScanSet = frameSet;
uimfRun.ResultCollection.MSPeakResultList.Clear();
foreach (var scanSet in IMSScanSetCollection.ScanSetList)
{
uimfRun.CurrentIMSScanSet = (IMSScanSet)scanSet;
MSGenerator.Execute(uimfRun.ResultCollection);
_ms1PeakDetector.Execute(uimfRun.ResultCollection);
}
peakExporter.WriteOutPeaks(sw, uimfRun.ResultCollection.MSPeakResultList);
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 1 || frameCounter == numTotalFrames)
{
lastProgress = DateTime.UtcNow;
var percentProgress = frameCounter * 100 / (double)numTotalFrames;
reportProgress(percentProgress);
}
}
}
else
{
var scanCounter = 0;
foreach (var scan in LcScanSetCollection.ScanSetList)
{
scanCounter++;
Run.CurrentScanSet = scan;
Run.ResultCollection.MSPeakResultList.Clear();
MSGenerator.Execute(Run.ResultCollection);
if (Run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
_ms1PeakDetector.Execute(Run.ResultCollection);
}
else
{
var dataIsCentroided = Run.IsDataCentroided(scan.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidedData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
}
peakExporter.WriteOutPeaks(sw, Run.ResultCollection.MSPeakResultList);
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 1 || scanCounter == numTotalScans)
{
lastProgress = DateTime.UtcNow;
var percentProgress = scanCounter * 100 / (double)numTotalScans;
reportProgress(percentProgress);
}
}
}
}
Run.ResultCollection.MSPeakResultList.Clear();
}
public override void Execute()
{
InitializeWorkflow();
PrepareOutputFolder(_workflowParameters.OutputFolder);
string outputPeaksFileName = getOutputPeaksFilename();
peakExporter = new PeakListTextExporter(Run.MSFileType, outputPeaksFileName);
int numTotalScans = Run.ScanSetCollection.ScanSetList.Count;
int scanCounter = 0;
if (Run.MSFileType == DeconTools.Backend.Globals.MSFileType.PNNL_UIMF)
{
var uimfrun = Run as UIMFRun;
int numTotalFrames = uimfrun.ScanSetCollection.ScanSetList.Count;
int frameCounter = 0;
foreach (var frameSet in uimfrun.ScanSetCollection.ScanSetList)
{
frameCounter++;
uimfrun.CurrentScanSet = frameSet;
uimfrun.ResultCollection.MSPeakResultList.Clear();
foreach (var scanSet in uimfrun.IMSScanSetCollection.ScanSetList)
{
uimfrun.CurrentIMSScanSet = (IMSScanSet)scanSet;
MSGenerator.Execute(uimfrun.ResultCollection);
this._ms1PeakDetector.Execute(uimfrun.ResultCollection);
}
peakExporter.WriteOutPeaks(uimfrun.ResultCollection.MSPeakResultList);
if (frameCounter % 5 == 0 || scanCounter == numTotalFrames)
{
double percentProgress = frameCounter * 100 / numTotalFrames;
reportProgress(percentProgress);
}
}
}
else
{
foreach (var scan in Run.ScanSetCollection.ScanSetList)
{
scanCounter++;
Run.CurrentScanSet = scan;
Run.ResultCollection.MSPeakResultList.Clear();
MSGenerator.Execute(Run.ResultCollection);
if (Run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
this._ms1PeakDetector.Execute(Run.ResultCollection);
}
else
{
var dataIsCentroided = Run.IsDataCentroided(scan.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidedData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
}
peakExporter.WriteOutPeaks(Run.ResultCollection.MSPeakResultList);
if (scanCounter % 50 == 0 || scanCounter == numTotalScans)
{
double percentProgress = scanCounter * 100 / numTotalScans;
reportProgress(percentProgress);
}
}
}
Run.ResultCollection.MSPeakResultList.Clear();
}
private void ExportPeaks_copied(string peaksfile)
{
DeconToolsPeakDetectorV2 _ms1PeakDetector;
DeconToolsPeakDetectorV2 _ms2PeakDetectorForCentroidedData;
DeconToolsPeakDetectorV2 _ms2PeakDetectorForProfileData;
var msGen = MSGeneratorFactory.CreateMSGenerator(_run.MSFileType);
_ms1PeakDetector = new DeconToolsPeakDetectorV2(2.0, 2.0,
DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false);
_ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(2.0,
2.0,
DeconTools.Backend.Globals.PeakFitType.QUADRATIC,
false);
_ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2(0, 0, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
_ms2PeakDetectorForCentroidedData.RawDataType = DeconTools.Backend.Globals.RawDataType.Centroided;
_ms2PeakDetectorForProfileData.PeaksAreStored = true;
_ms2PeakDetectorForCentroidedData.PeaksAreStored = true;
_ms1PeakDetector.PeaksAreStored = true;
var peakExporter = new PeakListTextExporter(_run.MSFileType, peaksfile);
var numTotalScans = _run.ScanSetCollection.ScanSetList.Count;
var scanCounter = 0;
if (_run.MSFileType == DeconTools.Backend.Globals.MSFileType.PNNL_UIMF)
{
var uimfrun = _run as UIMFRun;
var numTotalFrames = uimfrun.ScanSetCollection.ScanSetList.Count;
var frameCounter = 0;
foreach (var frameSet in uimfrun.ScanSetCollection.ScanSetList)
{
frameCounter++;
uimfrun.CurrentScanSet = frameSet;
uimfrun.ResultCollection.MSPeakResultList.Clear();
foreach (var scanSet in uimfrun.IMSScanSetCollection.ScanSetList)
{
uimfrun.CurrentIMSScanSet = (IMSScanSet)scanSet;
msGen.Execute(uimfrun.ResultCollection);
_ms1PeakDetector.Execute(uimfrun.ResultCollection);
}
peakExporter.WriteOutPeaks(uimfrun.ResultCollection.MSPeakResultList);
if (frameCounter % 5 == 0 || scanCounter == numTotalFrames)
{
double percentProgress = frameCounter * 100 / numTotalFrames;
// reportProgress(percentProgress);
}
}
}
else
{
foreach (var scan in _run.ScanSetCollection.ScanSetList)
{
scanCounter++;
_run.CurrentScanSet = scan;
_run.ResultCollection.MSPeakResultList.Clear();
msGen.Execute(_run.ResultCollection);
if (_run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
_ms1PeakDetector.Execute(_run.ResultCollection);
}
else
{
var dataIsCentroided = _run.IsDataCentroided(scan.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidedData.Execute(_run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(_run.ResultCollection);
}
}
peakExporter.WriteOutPeaks(_run.ResultCollection.MSPeakResultList);
}
}
}
public void updateScanResultsUIMFFileTest1()
{
UIMFRun run = new UIMFRun(uimfFilepath);
run.FrameSetCollection = new FrameSetCollection();
for (int i = 1200; i < 1203; i++)
{
run.FrameSetCollection.FrameSetList.Add(new FrameSet(i));
}
run.ScanSetCollection = new ScanSetCollection();
for (int i = 200; i < 304; i++)
{
run.ScanSetCollection.ScanSetList.Add(new ScanSet(i));
}
StreamWriter sw;
ResultCollection results = new ResultCollection(run);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task rapid = new RapidDeconvolutor();
Task scanResultUpdater = new ScanResultUpdater();
Task peakListExporter = new PeakListTextExporter(run.MSFileType, peakListoutputPath);
foreach (FrameSet frameset in run.FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frameset;
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
msgen.Execute(results);
peakDetector.Execute(results);
rapid.Execute(results);
scanResultUpdater.Execute(results);
peakListExporter.Execute(results);
}
}
peakListExporter.Cleanup();
Assert.AreEqual(3, results.ScanResultList.Count);
Assert.AreEqual(1, results.ScanResultList[0].SpectrumType);
Assert.AreEqual(670.990710325132, (decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(183, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(7097, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(-1, (decimal)results.ScanResultList[0].ScanTime);
UIMFScanResult uimfScanresult1 = (UIMFScanResult)(results.ScanResultList[0]);
Assert.AreEqual(4.0, uimfScanresult1.FramePressureFront);
Assert.AreEqual(4.016, uimfScanresult1.FramePressureBack);
Assert.AreEqual(1200, uimfScanresult1.Frameset.PrimaryFrame);
Assert.AreEqual(504, results.ResultList.Count);
}
