public MercuryDistributionCreator()
{
avergineFormulaCreator = new DeconToolsV2.HornTransform.clsAveragine();
hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
decon2LSMercuryDistribution = new DeconToolsV2.clsMercuryIsotopeDistribution();
peakDetector = new DeconToolsPeakDetector();
}
public void exporterTest1()
{
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(233);
ResultCollection results = new ResultCollection(run);
Task msGen = new GenericMSGenerator();
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
Task decon = new HornDeconvolutor(hornParams);
decon.Execute(results);
Exporter <ResultCollection> exporter = new BasicIsosExporter(exporterTest1OutputName);
exporter.Export(results);
}
public MercuryDistCollectionCreator()
{
this.hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
this.averagineFormula = this.hornParameters.AveragineFormula;
this.tagFormula = this.hornParameters.TagFormula;
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
Task msGen = new GenericMSGenerator(1154, 1158);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParameters.PeptideMinBackgroundRatio = 2;
Task decon = new HornDeconvolutor(hornParameters);
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
StringBuilder sb = new StringBuilder();
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0209385414928986, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void xcaliburFileMSMSDataTest1()
{
//exploring how only MSMS data is processed...
Project.Reset();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6004); //only MS/MS data here
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
sscc.Create();
Project project = Project.getInstance();
project.RunCollection.Add(run);
Task msGen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 1.3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 2;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornparams.PeptideMinBackgroundRatio = 2;
Task hornDecon = new HornDeconvolutor(hornparams);
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(hornDecon);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(3, project.TaskCollection.TaskList.Count);
// Assert.AreEqual(21, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(0, project.RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[0].ResultCollection.ResultList.Count);
}
public frmDecon2LS()
{
try
{
this.mMediator = new Decon2LSMediator(this);
//
// Required for Windows Form Designer support
//
InitializeComponent();
this.mMdiChildCloseHandler = new EventHandler(this.MdiChildClosed);
// attach file viewer to mediator
this.mFileTreeView.AttachTo(mMediator);
// Initialize the categories that we always want to appear in the side view
frmSpectra.InitializeCategories(mFileTreeView);
frmMercury.InitializeCategories(mFileTreeView);
frm2DPeakProcessing.InitializeCategories(mFileTreeView);
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
}
try
{
var paramLoader = new clsParameterLoader();
if (System.IO.File.Exists(Application.ExecutablePath + mstrDEFAULTPARAMFILE))
{
mstrParamFile = Application.ExecutablePath + mstrDEFAULTPARAMFILE;
paramLoader.LoadParametersFromFile(mstrParamFile);
mobjPeakParameters = paramLoader.PeakParameters;
mobjTransformParameters = paramLoader.TransformParameters;
mobjFTICRRawPreProcessParameters = paramLoader.FTICRPreprocessOptions;
mobjDTAGenerationParameters = paramLoader.DTAParameters;
}
else if (System.IO.File.Exists(Application.UserAppDataPath + mstrDEFAULTPARAMFILE))
{
mstrParamFile = Application.UserAppDataPath + mstrDEFAULTPARAMFILE;
paramLoader.LoadParametersFromFile(mstrParamFile);
mobjPeakParameters = paramLoader.PeakParameters;
mobjTransformParameters = paramLoader.TransformParameters;
mobjFTICRRawPreProcessParameters = paramLoader.FTICRPreprocessOptions;
mobjDTAGenerationParameters = paramLoader.DTAParameters;
}
else
{
// no default parameters found, loading defaults.
MessageBox.Show(this, "No parameter file found. Loading defaults.");
mobjPeakParameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
mobjTransformParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
mobjFTICRRawPreProcessParameters = new DeconToolsV2.Readers.clsRawDataPreprocessOptions();
mobjDTAGenerationParameters = new DeconToolsV2.DTAGeneration.clsDTAGenerationParameters();
mstrParamFile = Application.ExecutablePath + mstrDEFAULTPARAMFILE;
}
}
catch (Exception ex)
{
Console.WriteLine(ex.Message + ex.StackTrace);
mobjPeakParameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
mobjTransformParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
mobjFTICRRawPreProcessParameters = new DeconToolsV2.Readers.clsRawDataPreprocessOptions();
mobjDTAGenerationParameters = new DeconToolsV2.DTAGeneration.clsDTAGenerationParameters();
}
}
public void multiIMFFileDeconTest1()
{
imfFileList.Clear();
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_1.IMF");
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_2.IMF");
imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_SQ_14V_0000.Accum_1.IMF");
Project.Reset();
Project project = Project.getInstance();
foreach (string strItem in imfFileList)
{
Run run = new IMFRun(strItem, 233, 233);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1);
sscc.Create();
}
Task msGen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornparams.PeptideMinBackgroundRatio = 5;
Task hornDecon = new HornDeconvolutor(hornparams);
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(hornDecon);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Assert.AreEqual(3, Project.getInstance().RunCollection.Count);
Assert.AreEqual(3, project.TaskCollection.TaskList.Count);
Assert.AreEqual(1, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(12, project.RunCollection[0].ResultCollection.ResultList.Count);
int totalScans = 0;
int totalFeatures = 0;
for (int i = 0; i < project.RunCollection.Count; i++)
{
Console.WriteLine("Run name = " + project.RunCollection[i].Filename);
Console.WriteLine("Scans analyzed = " + project.RunCollection[i].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[i].ResultCollection.ResultList.Count);
totalFeatures += project.RunCollection[i].ResultCollection.ResultList.Count;
totalScans += project.RunCollection[i].ScanSetCollection.ScanSetList.Count;
}
Console.WriteLine("------------------------------------------------");
Console.WriteLine("Total Features found = " + totalFeatures);
Console.WriteLine("Total Scans = " + totalScans);
Console.WriteLine("Total Time required (ms) = " + sw.ElapsedMilliseconds);
}
public void multipleFrames_horn_test4()
{
Project.Reset();
//Project.getInstance().LoadOldDecon2LSParameters(uimfParameters1);
UIMFRun run = new UIMFRun(uimfFilepath, 1202, 1202);
Project.getInstance().RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 4;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParams.CompleteFit = true;
hornParams.LeftFitStringencyFactor = 2.5;
hornParams.RightFitStringencyFactor = 0.5;
hornParams.PeptideMinBackgroundRatio = 4;
hornParams.MaxFit = 0.4;
hornParams.UseMZRange = false;
hornParams.UseMercuryCaching = true;
Task decon = new HornDeconvolutor(hornParams);
Task scanResultsUpdater = new ScanResultUpdater();
Project.getInstance().TaskCollection.TaskList.Add(msGen);
Project.getInstance().TaskCollection.TaskList.Add(zeroFiller);
Project.getInstance().TaskCollection.TaskList.Add(peakDetector);
Project.getInstance().TaskCollection.TaskList.Add(decon);
Project.getInstance().TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(Project.getInstance().TaskCollection);
controller.Execute(Project.getInstance().RunCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + Project.getInstance().RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + Project.getInstance().RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks);
StringBuilder sb = new StringBuilder();
}
public void imf_multipleFrames_horn_test2()
{
List <Run> runCollection = new List <Run>();
Run run = new IMFRun(imfFilePath);
runCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
Task msGen = new GenericMSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 4;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParams.CompleteFit = true;
hornParams.LeftFitStringencyFactor = 2.5;
hornParams.RightFitStringencyFactor = 0.5;
hornParams.PeptideMinBackgroundRatio = 4;
hornParams.MaxFit = 0.4;
Task decon = new HornDeconvolutor(hornParams);
Task scanResultsUpdater = new ScanResultUpdater();
TaskCollection tc = new TaskCollection();
tc.TaskList.Add(msGen);
tc.TaskList.Add(zeroFiller);
tc.TaskList.Add(peakDetector);
tc.TaskList.Add(decon);
tc.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(tc);
controller.Execute(runCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + runCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + runCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + runCollection[0].ResultCollection.ScanResultList.Sum(p => p.NumPeaks));
StringBuilder sb = new StringBuilder();
}
public void xcaliburSpeed_THRASH_Test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
int startScan = 6005;
int stopScan = 6050;
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, startScan, stopScan, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection results = new ResultCollection(run);
List <timingResult> timingResults = new List <timingResult>();
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
if (results.Run.GetMSLevel(scanset.PrimaryScanNumber) != 1)
{
continue;
}
sw.Reset();
timingResult timeresult = new timingResult();
timeresult.frameNum = -1;
timeresult.scanNum = scanset.PrimaryScanNumber;
sw.Start();
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
timeresult.msGenTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
timeresult.peakDetectorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
Task decon = new HornDeconvolutor(hornParams);
decon.Execute(results);
timeresult.deconTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
timeresult.resultUpdaterTime = sw.ElapsedMilliseconds;
timingResults.Add(timeresult);
}
reportTimingEachScan(timingResults);
/*
* results on Gord's computer... 2009_11_18.
* scanNum msgen peakDet decon updater
* 6005 85 72 3013 3
* 6012 13 6 2661 0
* 6019 13 9 2908 0
* 6026 12 11 2560 0
* 6033 14 9 2778 0
* 6040 13 6 2558 0
* 6047 12 8 2753 0
*
* Avg: 23.1 17.3 2747.3 0.4
*/
}
