public void importIsosResultsAndFilterOnChargeStatesTest1()
{
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(xcaliburThrashIsos1, DeconTools.Backend.Globals.MSFileType.Finnigan);
Assert.AreEqual(11610, isosUtil.Results.Count);
List<IsosResult> chargeOneResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 1, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> chargeTwoResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 2, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> chargeThreeResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 3, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> chargeFourResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 4, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> chargeFiveResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 5, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> chargeSixResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 6, IsosResultUtilities.enumLinqOperator.EqualTo);
List<IsosResult> resultsWithChargeLessThan4 = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 4, IsosResultUtilities.enumLinqOperator.lessThan);
List<IsosResult> resultsWithChargeMoreThan6 = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 6, IsosResultUtilities.enumLinqOperator.greaterThan);
Assert.AreEqual(2323, chargeOneResultsOnly.Count);
Assert.AreEqual(5244, chargeTwoResultsOnly.Count);
Assert.AreEqual(2866, chargeThreeResultsOnly.Count);
Assert.AreEqual(946, chargeFourResultsOnly.Count);
Assert.AreEqual(153, chargeFiveResultsOnly.Count);
Assert.AreEqual(56, chargeSixResultsOnly.Count);
Assert.AreEqual(2323 + 5244 + 2866, resultsWithChargeLessThan4.Count);
Assert.AreEqual(22, resultsWithChargeMoreThan6.Count);
}
public void importLargeIsosFileTest1()
{
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(largeIsosFile1, DeconTools.Backend.Globals.MSFileType.Finnigan);
Assert.AreEqual(217847, isosUtil.Results.Count);
int count = IsosResultUtilities.getCount(isosUtil.Results);
Assert.AreEqual(200665, count);
List <IsosResult> chargeOneResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 1, IsosResultUtilities.enumLinqOperator.EqualTo);
List <IsosResult> chargeTwoResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 2, IsosResultUtilities.enumLinqOperator.EqualTo);
List <IsosResult> chargeThreeResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(isosUtil.Results, 3, IsosResultUtilities.enumLinqOperator.EqualTo);
Assert.AreEqual(27541, chargeOneResultsOnly.Count);
double avgScore = IsosResultUtilities.getAverageScore(chargeOneResultsOnly);
double stdev = IsosResultUtilities.getStdDevScore(chargeOneResultsOnly);
Console.WriteLine(avgScore);
Console.WriteLine(stdev);
}
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 test2()
{
IsosResultComparer comparer = new IsosResultComparer();
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(xcaliburThrashIsos1, DeconTools.Backend.Globals.MSFileType.Finnigan);
IsosResultUtilities isosUtil2 = new IsosResultUtilities();
isosUtil2.LoadResults(xcaliburThrashIsos1, DeconTools.Backend.Globals.MSFileType.Finnigan);
List <IsosResult> resultList1 = isosUtil.Results.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();
List <IsosResult> resultList2 = isosUtil2.Results.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();;
Assert.AreEqual(86, resultList1.Count);
Assert.AreEqual(86, resultList2.Count);
resultList1.RemoveAt(30);
resultList1.RemoveAt(30);
resultList1.RemoveAt(30);
resultList2.RemoveAt(0);
resultList2.RemoveAt(0);
resultList2.RemoveAt(0);
resultList2.RemoveAt(0);
Assert.AreEqual(86 - 4, resultList2.Count);
Assert.AreEqual(86 - 3, resultList1.Count);
List <IsosResult> intersectedList = comparer.GetIntersectionBetweenTwoIsosResultSets(resultList1, resultList2);
Assert.AreEqual(86 - 7, intersectedList.Count);
}
public void test1_summing()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1201);
project.RunCollection.Add(run);
int numFramesSummed = 3;
int numScansSummed = 3;
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, numScansSummed, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, numFramesSummed, 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;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
project.TaskCollection.TaskList.Add(originalIntensitiesExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
ResultCollection rc = project.RunCollection[0].ResultCollection;
Assert.AreEqual(180, rc.ResultList.Count);
StringBuilder sb = new StringBuilder();
IsosResultUtilities.DisplayResults(sb, rc.ResultList);
Console.Write(sb.ToString());
}
public void getAverageScoreTest1()
{
TestUtilities testUtils = new TestUtilities();
List <IsosResult> thrashResults = testUtils.CreateThrashIsosResults1();
outputFitValuesToConsole(thrashResults);
double avgFit = IsosResultUtilities.getAverageScore(thrashResults);
Assert.AreEqual(0.0482473459193904, (decimal)avgFit);
}
public void loadIMFResultsAndThenExport()
{
IsosResultUtilities iru = new IsosResultUtilities();
List <IsosResult> results = iru.getIMFResults(imfIsosFolder, 500, 600);
UIMFIsosExporter exporter = new UIMFIsosExporter(Path.Combine(imfIsosFolder, "mergedIsosResults.csv"));
ResultCollection rc = new ResultCollection(new IMFRun());
rc.ResultList = results;
exporter.Export(rc);
}
public void getSpecificChargeStateResultsOnlyTest1()
{
TestUtilities testUtils = new TestUtilities();
List <IsosResult> thrashResults = testUtils.CreateThrashIsosResults1();
List <IsosResult> chargeTwoResultsOnly = IsosResultUtilities.getIsosResultsByChargeState(thrashResults, 2, IsosResultUtilities.enumLinqOperator.EqualTo);
foreach (IsosResult result in chargeTwoResultsOnly)
{
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
}
Assert.AreEqual(136, chargeTwoResultsOnly.Count);
double avgFit = IsosResultUtilities.getAverageScore(chargeTwoResultsOnly);
Assert.AreEqual(0.0490575547734101m, (decimal)avgFit);
}
public void loadIMFIsosResultTest1()
{
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(imfIsos1, DeconTools.Backend.Globals.MSFileType.PNNL_IMS);
Assert.AreEqual(43, isosUtil.Results.Count);
IsosResult imfTestResult1 = isosUtil.Results[3];
Assert.AreEqual(231, imfTestResult1.ScanSet.PrimaryScanNumber);
Assert.AreEqual(2, imfTestResult1.IsotopicProfile.ChargeState);
Assert.AreEqual(7768, imfTestResult1.IsotopicProfile.GetAbundance());
//Assert.AreEqual(432.92416, uimfTestResult1.IsotopicProfile.GetMZofMostAbundantPeak());
Assert.AreEqual(0.0098, imfTestResult1.IsotopicProfile.Score);
//Assert.AreEqual(1142.4074, uimfTestResult1.IsotopicProfile.AverageMass);
Assert.AreEqual(1141.7091, imfTestResult1.IsotopicProfile.MonoIsotopicMass);
Assert.AreEqual(0.0633,Math.Round(imfTestResult1.IsotopicProfile.GetFWHM(),4));
Assert.AreEqual(112.58, Math.Round(imfTestResult1.IsotopicProfile.GetSignalToNoise(),2));
//231,2,7768,571.8613,0.0098,1142.4074,1141.7091,1141.7091,0.0633,112.58,7768,1640
}
public void compareThrashRapidTest1()
{
IsosResultComparer comparer = new IsosResultComparer();
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(isosByThrash1, DeconTools.Backend.Globals.MSFileType.Finnigan);
IsosResultUtilities isosUtil2 = new IsosResultUtilities();
isosUtil2.LoadResults(isosByRapid1, DeconTools.Backend.Globals.MSFileType.Finnigan);
List <IsosResult> rapidResults = isosUtil2.Results;
List <IsosResult> thrashResults = isosUtil.Results;
Console.WriteLine("Thrash result count = " + thrashResults.Count);
Console.WriteLine("RAPID result count = " + rapidResults.Count);
List <IsosResult> intersectedResults = comparer.GetIntersectionBetweenTwoIsosResultSets(thrashResults, rapidResults);
//List<IsosResult> intersectedResults2 = comparer.GetIntersectionTheManualWay(thrashResults, rapidResults);
//List<IsosResult> intersectedResults3 = comparer.GetIntersectionTheManualWay(rapidResults, thrashResults);
List <IsosResult> unmatchedResults1 = comparer.GetUniqueBetweenTwoIsosResultSets(rapidResults, thrashResults);
List <IsosResult> unmatchedResults2 = comparer.GetUniqueBetweenTwoIsosResultSets(thrashResults, rapidResults);
Console.WriteLine("Intersected result count = " + intersectedResults.Count);
//Console.WriteLine("Manual Intersected result count = " + intersectedResults2.Count);
//Console.WriteLine("Manual Intersected result count = " + intersectedResults3.Count);
Console.WriteLine("unmatched result count = " + unmatchedResults1.Count);
Console.WriteLine("unmatched result count2 = " + unmatchedResults2.Count);
}
public void compareRAWData_cacheONvs_cacheOffTest1()
{
IsosResultComparer comparer = new IsosResultComparer();
IsosResultUtilities isosUtil = new IsosResultUtilities();
isosUtil.LoadResults(rawIsosCacheOnCompleteFitOFF, DeconTools.Backend.Globals.MSFileType.Finnigan);
IsosResultUtilities isosUtil2 = new IsosResultUtilities();
isosUtil2.LoadResults(rawIsosCacheOFFCompleteFitOFF, DeconTools.Backend.Globals.MSFileType.Finnigan);
List <IsosResult> cacheOnResults = isosUtil.Results;
List <IsosResult> cacheOffResults = isosUtil2.Results;
Console.WriteLine("cache on count = " + cacheOnResults.Count);
Console.WriteLine("cache off count = " + cacheOffResults.Count);
List <IsosResult> intersectedResults = comparer.GetIntersectionBetweenTwoIsosResultSets(cacheOffResults, cacheOnResults);
List <IsosResult> unmatchedResults1 = comparer.GetUniqueBetweenTwoIsosResultSets(cacheOnResults, cacheOffResults);
List <IsosResult> unmatchedResults2 = comparer.GetUniqueBetweenTwoIsosResultSets(cacheOffResults, cacheOnResults);
List <IsosResult> intersectedResults2 = comparer.GetIntersectionTheManualWay(cacheOnResults, cacheOffResults);
//List<IsosResult> intersectedResults3 = comparer.GetIntersectionTheManualWay(rapidResults, thrashResults);
Console.WriteLine("Intersected result count = " + intersectedResults.Count);
Console.WriteLine("unmatched result count = " + unmatchedResults1.Count);
Console.WriteLine("unmatched result count2 = " + unmatchedResults2.Count);
Console.WriteLine("Manual Intersected result count = " + intersectedResults2.Count);
//Console.WriteLine("Manual Intersected result count = " + intersectedResults3.Count);
}
public void Generate3dBpiFromIsosFile1()
{
var outputOrigIntensity = false;
var outputToConsole = true;
var isosFile =
@"D:\Data\UIMF\Sarc_P13_C10_1186_23Sep11_Cheetah_11-09-06_isos.csv";
var outputFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2013\Saturation_Correction\chromOuputSatCorrected.txt";
var lcScanStart = 450;
var lcScanStop = 550;
var isosResultUtilities = new IsosResultUtilities();
var filteredIsos = isosResultUtilities.getUIMFResults(isosFile, lcScanStart, lcScanStop);
var outputIsosFilename = isosFile.Replace("_isos.csv", "_frame450-550_isos.csv");
var indexFrameCol = 1;
isosResultUtilities.FilterAndOutputIsos(isosFile, indexFrameCol, lcScanStart, lcScanStop, outputIsosFilename);
var imsScanStart = 60;
var imsScanStop = 250;
var startFrameIndex = 0;
using (var writer = new StreamWriter(outputFile))
{
for (var scan = lcScanStart; scan <= lcScanStop; scan++)
{
//Console.WriteLine("Frame = " + scan);
var lcScanResults = (from n in filteredIsos where n.ScanSet.PrimaryScanNumber == scan select n).ToList();
var sb = new StringBuilder();
for (var imsScan = imsScanStart; imsScan <= imsScanStop; imsScan++)
{
var imsScanResults =
(from n in lcScanResults
where ((UIMFIsosResult)n).IMSScanSet.PrimaryScanNumber == imsScan
orderby((UIMFIsosResult)n).IntensityAggregate descending
select n).ToList();
var basePeakIntensity = 0;
if (imsScanResults.Count == 0)
{
}
else
{
if (outputOrigIntensity)
{
basePeakIntensity = (int)imsScanResults.First().IsotopicProfile.getMostIntensePeak().Height;
}
else
{
basePeakIntensity = (int)imsScanResults.First().IntensityAggregate;
}
}
sb.Append(basePeakIntensity);
if (imsScan != imsScanStop)
{
sb.Append("\t");
}
}
writer.WriteLine(sb.ToString());
if (outputToConsole)
{
Console.WriteLine(sb.ToString());
}
}
}
}
