public void FailureToFindAnyChromatogramDataTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromGenTolerance = 1; //very narrow tolerance
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.EmpiricalFormula = DeconTools.Backend.Utilities.IsotopeDistributionCalculation.IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(1399);
target.ElutionTimeTheor = 0.3;
target.ChargeState = 1;
target.DoWorkflow();
var result = target.GetResult();
Assert.IsTrue(result.Target.TheorIsotopicProfile != null);
Assert.IsTrue(result != null);
Assert.IsTrue(result.IqResultDetail.Chromatogram == null);
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
public void IqWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
Console.WriteLine(target.EmpiricalFormula + "\t" + target.ChargeState);
target.DoWorkflow();
var result = target.GetResult();
Assert.IsNotNull(result, "result is null");
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}