public void featuresFoundByTargetedProcessing_thenAligned_test1()
{
string peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1;
Console.WriteLine("loading peaks.");
Run run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, peaksTestFile);
Console.WriteLine("done.");
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.ChromToleranceInPPM = 25;
parameters.ChromGeneratorMode = Backend.ProcessingTasks.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromPeakDetectorPeakBR = 2;
parameters.ChromPeakDetectorSigNoise = 2;
parameters.MSToleranceInPPM = 25;
TargetedAligner aligner = new TargetedAligner(run, parameters);
aligner.UpperFitScoreAllowedCriteria = 0.1;
aligner.IScoreAllowedCriteria = 0.15;
Console.WriteLine("Loading Mass tags...");
aligner.SetMassTags(massTagFile);
Console.WriteLine("Done.");
aligner.Execute();
}
public void featuresLoadedFromFile_test1()
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
TargetedAligner aligner = new TargetedAligner(run, parameters);
aligner.SetMassTags(massTagFile);
aligner.ImportedFeaturesFilename = deconToolsResultFile;
aligner.Execute();
}
