public void loadUIMFIsosResults_loadOneFrameOnly_Test1()
{
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(uimfIsos1, DeconTools.Backend.Globals.MSFileType.PNNL_UIMF,500);
Assert.AreEqual(1346, isosUtil.Results.Count);
UIMFIsosResult uimfTestResult1 = (UIMFIsosResult)isosUtil.Results[3];
Assert.AreEqual(1200, uimfTestResult1.FrameSet.PrimaryFrame);
Assert.AreEqual(250, uimfTestResult1.ScanSet.PrimaryScanNumber);
Assert.AreEqual(3, uimfTestResult1.IsotopicProfile.ChargeState);
Assert.AreEqual(1288, uimfTestResult1.IsotopicProfile.GetAbundance());
//Assert.AreEqual(432.92416, uimfTestResult1.IsotopicProfile.GetMZofMostAbundantPeak());
Assert.AreEqual(0.1458, uimfTestResult1.IsotopicProfile.Score);
//Assert.AreEqual(1296.54608, uimfTestResult1.IsotopicProfile.AverageMass);
Assert.AreEqual(1295.75229, uimfTestResult1.IsotopicProfile.MonoIsotopicMass);
Assert.AreEqual(0.0548, Math.Round(uimfTestResult1.IsotopicProfile.GetFWHM(), 4));
Assert.AreEqual(92, uimfTestResult1.IsotopicProfile.GetSignalToNoise());
//Assert.AreEqual(1200, uimfTestResult1.FrameSet.PrimaryFrame);
//250 3 1288 432.92416 0.1458 1296.54608 1295.75229 1295.75229 0.0548 92
}
public void deserializerGetResultsTest3()
{
ResultCollection results;
IsosResultDeSerializer deserializer = new IsosResultDeSerializer(deserializerUIMFTestFile1);
int counter = 0;
do
{
counter++;
results = deserializer.GetNextSetOfResults();
if (results != null)
{
StringBuilder sb = new StringBuilder();
foreach (IsosResult result in results.ResultList)
{
UIMFIsosResult uimfResult = (UIMFIsosResult)result;
sb.Append(uimfResult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.GetMZ());
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.GetAbundance());
sb.Append("\n");
}
Console.WriteLine("----------------------------------------------------------------------");
Console.Write(sb.ToString());
}
} while (results != null);
Assert.AreEqual(8, counter);
}
/// <summary>
/// This test ensures that the orig_intens data is the same as the data stored in the IsosResult when there is no summing
/// </summary>
//[Test]
//public void test1_nosumming()
//{
// Project.Reset();
// Project project = Project.getInstance();
// UIMFRun run = new UIMFRun(uimfFilepath, 1200, 1200);
// project.RunCollection.Add(run);
// ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, 1, 1);
// sscc.Create();
// FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
// fscc.Create();
// Task msGen = new UIMF_MSGenerator(200, 2000);
// 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);
// Task decon = new HornDeconvolutor();
// Task scanResultsUpdater = new ScanResultUpdater();
// project.TaskCollection.TaskList.Add(msGen);
// project.TaskCollection.TaskList.Add(peakDetector);
// project.TaskCollection.TaskList.Add(decon);
// project.TaskCollection.TaskList.Add(scanResultsUpdater);
// TaskController controller = new UIMF_TaskController(project.TaskCollection);
// controller.Execute(project.RunCollection);
// ResultCollection results = project.RunCollection[0].ResultCollection;
// OriginalIntensitiesExtractor origIntensExtractor = new OriginalIntensitiesExtractor(results);
// List<OriginalIntensitiesDTO> data = origIntensExtractor.ExtractOriginalIntensities();
// Assert.AreEqual(20, results.ResultList.Count);
// Assert.AreEqual(20, data.Count);
// //for (int i = 0; i < data.Count; i++)
// //{
// // Assert.AreEqual(results.ResultList[i].IsotopicProfile.GetAbundance(), data[i].originalIntensity);
// // Assert.AreEqual(results.ResultList[i].IsotopicProfile.GetSummedIntensity(), data[i].totIsotopicOrginalIntens);
// //}
// StringBuilder sb = new StringBuilder();
// reportOriginalIntensityData(sb, results.ResultList, data);
// Console.Write(sb.ToString());
//}
private void reportOriginalIntensityData(StringBuilder sb, List <IsosResult> results, List <OriginalIntensitiesDTO> origIntensdata)
{
int counter = 0;
sb.Append("scan\tmz\tabundance\tTIA\torig_intens\torigIntenseTIA\n");
foreach (OriginalIntensitiesDTO item in origIntensdata)
{
UIMFIsosResult result = (UIMFIsosResult)results[counter];
sb.Append(result.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(result.IsotopicProfile.GetMZ());
sb.Append("\t");
sb.Append(result.IsotopicProfile.GetAbundance());
sb.Append("\t");
sb.Append(result.IsotopicProfile.GetSummedIntensity());
sb.Append("\t");
sb.Append(item.originalIntensity);
sb.Append("\t");
sb.Append(item.totIsotopicOrginalIntens);
sb.Append("\n");
counter++;
}
}
public void uimf_data_preLoaded() // in this case, data is preloaded, preventing re-accessing the same drifttimes over and over
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
((UIMFRun)run).GetFrameDataAllFrameSets(); // this is the key line... loads data necessary for drift time calc and correction
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public void uimf_data_not_preLoaded() // in this case the drift time is calculated every time by looking up sqlite data from uimf file
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public List <IsosResult> convertIMFResultsToUIMFResults(int currentFrame, List <IsosResult> list)
{
var returnedResults = new List <IsosResult>();
foreach (var result in list)
{
var uimfResult = new UIMFIsosResult();
uimfResult.ScanSet = new LCScanSetIMS(currentFrame);
uimfResult.IsotopicProfile = result.IsotopicProfile;
uimfResult.Run = result.Run;
uimfResult.ScanSet = result.ScanSet;
returnedResults.Add(uimfResult);
}
return(returnedResults);
}
private IsosResult convertTextToIsosResult(List <string> processedData, List <string> headers)
{
IsosResult result;
if (fileType == Globals.MSFileType.PNNL_UIMF)
{
result = new UIMFIsosResult();
}
else
{
result = new StandardIsosResult();
}
result.IsotopicProfile = new IsotopicProfile();
//result.Run = getRunFromIsosFilename(this.importFilename, this.fileType); AM commenting this out since this gives me an error
//get ScanSet number from file
if (fileType == Globals.MSFileType.PNNL_UIMF)
{
var imsScanNum = parseIntField(lookup(processedData, headers, "ims_scan_num"));
var frame_num = parseIntField(lookup(processedData, headers, "frame_num"));
((UIMFIsosResult)result).DriftTime = parseDoubleField(lookup(processedData, headers, "drift_time"));
result.ScanSet = new LCScanSetIMS(frame_num);
((UIMFIsosResult)result).IMSScanSet = new IMSScanSet(imsScanNum);
}
else
{
var scan_num = parseIntField(lookup(processedData, headers, "scan_num"));
result.ScanSet = new ScanSet(scan_num);
}
result.IsotopicProfile.ChargeState = parseIntField(lookup(processedData, headers, "charge"));
result.IsotopicProfile.MonoIsotopicMass = parseDoubleField(lookup(processedData, headers, "monoisotopic_mw"));
result.IsotopicProfile.Score = parseDoubleField(lookup(processedData, headers, "fit"));
result.IntensityAggregate = parseFloatField(lookup(processedData, headers, "abundance"));
//result.IsotopicProfile.IntensityMostAbundant = parseFloatField(lookup(processedData, headers, "abundance"));
result.IsotopicProfile.MonoPeakMZ = parseDoubleField(lookup(processedData, headers, "mz"));
result.InterferenceScore = parseDoubleField(lookup(processedData, headers, "interference_score"));
result.IsotopicProfile.OriginalIntensity = parseDoubleField(lookup(processedData, headers, "unsummed_intensity"));
var saturationFlagString = lookup(processedData, headers, "saturation_flag");
result.IsotopicProfile.IsSaturated = saturationFlagString == "1";
var mz = parseFloatField(lookup(processedData, headers, "mz"));
var intensity = parseIntField(lookup(processedData, headers, "mono_abundance"));
var peak = new MSPeak(mz, intensity)
{
Width = parseFloatField(lookup(processedData, headers, "fwhm")),
SignalToNoise = parseFloatField(lookup(processedData, headers, "signal_noise"))
};
//mono mz isn't available from _isos file AM modification, while this is true, we still need this.
var flagString = lookup(processedData, headers, "flag");
if (string.IsNullOrEmpty(flagString))
{
}
else
{
var flagNum = parseIntField(flagString);
if (flagNum == 1)
{
result.Flags.Add(new PeakToTheLeftResultFlag()); // TODO: it'll be good to make a factory class for creating flags.
}
}
result.IsotopicProfile.Peaklist.Add(peak);
return(result);
}
public void test1()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1200, 1202);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(200, 2000);
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);
Task rapidDecon = new RapidDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
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);
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(4, project.TaskCollection.TaskList.Count);
Assert.AreEqual(600, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
UIMFRun uimfRun = (UIMFRun)(project.RunCollection[0]);
Assert.AreEqual(3, uimfRun.FrameSetCollection.FrameSetList.Count);
StringBuilder sb = new StringBuilder();
foreach (IsosResult result in project.RunCollection[0].ResultCollection.ResultList)
{
Assert.IsInstanceOfType(typeof(UIMFIsosResult), result);
UIMFIsosResult uimfResult = (UIMFIsosResult)result;
sb.Append(uimfResult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.Peaklist[0].XValue);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.GetAbundance());
sb.Append("\t");
//sb.Append(uimfResult.IsotopicProfile.
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
