public void testVladsData()
{
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndAlignRun(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24653;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as O16O18TargetedResultObject;
Assert.IsTrue(workflow.Success);
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
Console.WriteLine("Correlation between 016 and O18(double label)= " + result.ChromCorrO16O18DoubleLabel);
Assert.IsTrue(result.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment);
}
public void findSingleMassTag_test1()
{
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 6643962;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(6865, result.ScanSet.PrimaryScanNumber);
}
public void Test1()
{
var testFile = @"\\protoapps\UserData\Slysz\Data\O16O18\BSA\BSA_18O_99_8Jan11_Falcon_10-12-09.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\BSA\Targets\BSAmassTags_MinimalInfo_withScans.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 3;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.MostIntense;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromSmootherNumPointsInSmooth = 31;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
Assert.IsTrue(workflow.Result.Target.ScanLCTarget > 0);
Assert.IsNotNull(workflow.ChromPeakSelected);
Assert.AreEqual(10622, (int)workflow.ChromPeakSelected.XValue);
Console.WriteLine("ChromPeak scan value = " + workflow.ChromPeakSelected.XValue);
}
public void checkO16O18ChromGenMode_test1()
{
//
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 20746149;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
result.DisplayToConsole();
// Assert.AreEqual(3498, result.ScanSet.PrimaryScanNumber);
Console.WriteLine("O16O18 ChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Console.WriteLine("MonoChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
result.DisplayToConsole();
}