public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
ProjectBase project = TestHelper.CreateTestProject();
experiment = project.Experiments.First() as Experiment;
viewModel = new LabelingViewModel(experiment.Labeling.First(), experiment.ProteinStates.First(), experiment, mockServiceLocator.Object);
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
mockEventAggregator = new Mock<IEventAggregator>();
experiment = TestHelper.GetTestExperiment(mockServiceLocator);
run = new Run(Path.GetFileName(Properties.Settings.Default.mzXMLTestFile1), Properties.Settings.Default.mzXMLTestFile1, new ProteinState(experiment), new Labeling(experiment), experiment, new ProteoWizardDataProvider(mockEventAggregator.Object));
}
private static DeuterationResult GenerateDeuterationResult(Peptide peptide, ProteinState proteinState, Labeling labeling, Experiment experiment, Result result)
{
List<RunResult> replicates = new List<RunResult>();
foreach (Run run in experiment.GetRunsByProteinState(proteinState))
{
if (run.Labeling == labeling)
{
RunResult runResult = experiment.GetRunResult(result, run, peptide);
if (runResult != null)
{
replicates.Add(runResult);
}
}
}
DeuterationResult deuterationResult = new DeuterationResult(peptide, proteinState, labeling, replicates);
deuterationResult.AmountDeut = Math.Round(MathUtility.GetAverage(deuterationResult.DeuterationValues), 5);
deuterationResult.AmountDeuterationStandardDeviation = Math.Round(MathUtility.GetStandardDeviation(deuterationResult.DeuterationValues), 5);
deuterationResult.AmountDeuterationFromDeuterationDistribution = Math.Round(MathUtility.GetAverage(deuterationResult.DeuterationDistributedDeuterationValues), 5);
deuterationResult.AmountDeuterationFromDeuterationDistributionStandardDeviation = Math.Round(MathUtility.GetStandardDeviation(deuterationResult.DeuterationDistributedDeuterationValues), 5);
deuterationResult.CentroidMass = Math.Round(MathUtility.GetAverage(deuterationResult.CentroidMassValues), 5);
deuterationResult.CentroidMassStandardDeviation = Math.Round(MathUtility.GetStandardDeviation(deuterationResult.CentroidMassValues), 5);
if (replicates.Count > 0)
{
deuterationResult.TheoreticalCentroidMass = Math.Round(replicates.Average(item => item.TheoreticalAverageMass), 5);
}
return deuterationResult;
}
public SelectTemplateViewModel(Experiment experiment, IServiceLocator serviceLocator)
{
this.experiment = experiment;
this.serviceLocator = serviceLocator;
_selectedDataPath = Properties.Settings.Default.LastBrowseTemplateDataPath;
LoadRecentLocations();
}
public Result(string name, Experiment experiment)
: this()
{
_experiment = experiment;
_name = name;
_location = "Results - " + DateTime.Now.ToString("yyyy-MM-dd hh.mm.ss") + ".xml";
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
project = TestHelper.CreateTestProject();
experiment = project.Experiments.First() as Experiment;
viewModel = new PeptidesViewModel(project.Experiments.First() as Experiment, mockServiceLocator.Object);
Assert.AreEqual(2, viewModel.Children.Count);
}
public Run(string filename, string fullPath, ProteinState proteinState, Labeling labeling, Experiment experiment, IDataProvider dataProvider)
: base(filename, fullPath, dataProvider)
{
ProteinState = proteinState;
Labeling = labeling;
Experiment = experiment;
experiment.Runs.Add(this);
}
public HydraTemplateWizardController(IRegionManager regionManager, IServiceLocator serviceLocator, Experiment experiment)
{
_regionManager = regionManager;
_experiment = experiment;
_serviceLocator = serviceLocator;
_wizardViewModels = new List<WizardStepViewModel>();
SelectTemplateViewModel templateViewModel = new SelectTemplateViewModel(experiment, serviceLocator);
_wizardViewModels.Add(templateViewModel);
}
public void CreateDirectoryStructure()
{
Assert.IsFalse(Directory.Exists(TestExperimentDirectory));
Experiment experiment = new Experiment(TestExperimentName, new MassSpecStudio.Core.Domain.ProjectBase("temp", @"C:\"), new HydraExperimentType(mockServiceLocator.Object));
experiment.CreateDirectoryStructure();
Assert.IsTrue(Directory.Exists(TestExperimentDirectory));
Assert.IsTrue(Directory.Exists(Path.Combine(TestExperimentDirectory, "Data")));
Assert.IsTrue(Directory.Exists(Path.Combine(TestExperimentDirectory, "Results")));
}
public static WizardViewModel CreateController(Experiment experiment, IRegionManager regionManager, IServiceLocator serviceLocator)
{
if (experiment.ExperimentTypeObject is TemplatedHydraExperimentType)
{
return new HydraTemplateWizardController(regionManager, serviceLocator, experiment);
}
else
{
return new HydraExperimentWizardController(regionManager, serviceLocator, experiment);
}
}
public void TestInitialize()
{
mockEventAggregator = new Mock<IEventAggregator>();
mockServiceLocator = new Mock<IServiceLocator>();
mockServiceLocator.Setup(mock => mock.GetAllInstances<IDataProvider>()).Returns(new List<IDataProvider>() { new ProteoWizardDataProvider(mockEventAggregator.Object) });
ProjectBase project = TestHelper.CreateTestProject();
experiment = project.Experiments.First() as Experiment;
experimentViewModel = new ExperimentViewModel(experiment);
viewModel = new DataProviderViewModel(experimentViewModel, mockServiceLocator.Object);
}
public void TestInitialize()
{
IXYData xyData = new XYData(new double[] { 1, 2 }, new double[] { 3, 4 });
mockServiceLocator = new Mock<IServiceLocator>();
mockEventAggregator = new Mock<IEventAggregator>();
mockDataProvider = new Mock<IDataProvider>();
mockDataProvider.Setup(mock => mock.GetTotalIonChromatogram(TimeUnit.Seconds)).Returns(xyData);
mockDataProvider.Setup(mock => mock.GetExtractedIonChromatogram(2, 2, 0.5, TimeUnit.Seconds)).Returns(xyData);
mockDataProvider.Setup(mock => mock.GetSpectrum(2, 3, 3, 6, 0)).Returns(xyData);
experiment = Test.TestHelper.GetTestExperiment(mockServiceLocator);
run = new Run(Path.GetFileName(Properties.Settings.Default.mzXMLTestFile1), Properties.Settings.Default.mzXMLTestFile1, new ProteinState(experiment), new Labeling(experiment), experiment, mockDataProvider.Object);
}
public HydraExperimentWizardController(IRegionManager regionManager, IServiceLocator serviceLocator, Experiment experiment)
{
_regionManager = regionManager;
_experiment = experiment;
_serviceLocator = serviceLocator;
_wizardViewModels = new List<WizardStepViewModel>();
ExperimentViewModel experimentViewModel = new ExperimentViewModel(experiment);
_wizardViewModels.Add(new ProteinStatesViewModel(experimentViewModel));
_wizardViewModels.Add(new LabellingsViewModel(experimentViewModel));
_wizardViewModels.Add(new DataProviderViewModel(experimentViewModel, serviceLocator));
_wizardViewModels.Add(new RunsViewModel(experimentViewModel));
_wizardViewModels.Add(new ImportPeptidesViewModel(experimentViewModel));
}
private string GetNextName(Experiment experiment)
{
int maximumCount = 0;
foreach (ProteinState proteinState in experiment.ProteinStates.Where(item => item.Name.ToLower().StartsWith("protein state")).OrderBy(item => item.Name))
{
int result = 0;
if (Int32.TryParse(proteinState.Name.ToLower().Replace("protein state", string.Empty), out result))
{
maximumCount = result > maximumCount ? result : maximumCount;
}
}
return "Protein state " + (maximumCount + 1);
}
public void Execute(Experiment experiment, Result result)
{
_output.Publish("- Calculating Deuteration Results");
result.DeuterationResults = new List<DeuterationResult>();
foreach (Peptide peptide in experiment.Peptides.PeptideCollection)
{
foreach (ProteinState proteinState in experiment.ProteinStates)
{
foreach (Labeling labeling in experiment.Labeling)
{
result.DeuterationResults.Add(GenerateDeuterationResult(peptide, proteinState, labeling, experiment, result));
}
}
}
_output.Publish("- Deuteration Results Calculation Complete");
}
public void TestInitialize()
{
mockEventAggregator = new Mock<IEventAggregator>();
mockServiceLocator = new Mock<IServiceLocator>();
mockServiceLocator.Setup(mock => mock.GetAllInstances<IDataProvider>()).Returns(new List<IDataProvider>() { new ProteoWizardDataProvider(mockEventAggregator.Object) });
experiment = TestHelper.GetTestExperiment(mockServiceLocator);
try
{
if (Directory.Exists(TestExperimentDirectory))
{
Directory.Delete(TestExperimentDirectory, true);
}
}
catch
{
// Do Nothing
}
}
public void TestInitialize()
{
project = TestHelper.CreateTestProject();
viewModel = new ProjectViewModel(project);
samplesViewModel = viewModel.Children.First().Children.First() as SamplesViewModel;
experiment = (Experiment)project.Experiments.First();
}
private void OpenExperiment()
{
experiment = Experiment.Open(Properties.Settings.Default.TestExperiment1, new MassSpecStudio.Core.Domain.ProjectBase("testProject1", Properties.Settings.Default.ProjectRootDirectory), mockServiceLocator.Object);
}
private static Hydra.Core.Domain.Run CreateRun(string filename, ProteinState proteinState, Labeling labeling, Experiment experiment, Mock<IEventAggregator> mockEventAggregator)
{
string runFileName = Path.GetFileName(filename);
File.Copy(filename, Path.Combine(TestExperimentDirectory, "Data", runFileName), true);
Hydra.Core.Domain.Run run = new Hydra.Core.Domain.Run(
@"Data\" + runFileName,
Path.Combine(TestExperimentDirectory, "Data", runFileName),
proteinState,
labeling,
experiment,
new ProteoWizardDataProvider(mockEventAggregator.Object));
return run;
}
public static Result Open(Experiment experiment, string path)
{
DataContractSerializer serializer = new DataContractSerializer(typeof(Result));
using (XmlReader stream = XmlReader.Create(Path.Combine(GetFullPath(experiment), path)))
{
Result result = serializer.ReadObject(stream, true) as Result;
result.Location = path;
result._experiment = experiment;
foreach (RunResult runResult in result.RunResults)
{
runResult.Run = experiment.Runs.Where(item => item.FileName == runResult.Run.FileName).FirstOrDefault();
}
return result;
}
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
experiment = TestHelper.GetTestExperiment(mockServiceLocator);
proteinState = new ProteinState(experiment);
}
private static string GetFullPath(Experiment experiment)
{
return Path.Combine(Path.GetDirectoryName(experiment.Location), "Results");
}
protected ExperimentBase CreateExperimentFile(ProjectBase project, string experimentName)
{
string experimentDirectory = Path.Combine(project.Directory, experimentName);
Experiment experiment = new Experiment(experimentName, project, this);
experiment.Save();
return experiment;
}
public void Save(Experiment experiment)
{
experiment.Save();
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
experiment = TestHelper.GetTestExperiment(mockServiceLocator);
labeling = new Labeling(experiment);
}
private void SetNextPercentAndTime(Experiment experiment)
{
Labeling maxLabelingPercentage = experiment.Labeling.OrderByDescending(item => item.LabelingPercent).FirstOrDefault();
if (maxLabelingPercentage != null)
{
if ((maxLabelingPercentage.LabelingPercent + 10) > 100)
{
LabelingPercent = 100;
}
else
{
LabelingPercent = maxLabelingPercentage.LabelingPercent + 10;
}
LabelingTime = maxLabelingPercentage.LabelingTime + 1;
}
else
{
LabelingPercent = 20;
LabelingTime = 1;
}
}
public ProteinState(Experiment parentExperiment)
{
_name = GetNextName(parentExperiment);
_parentExperiment = parentExperiment;
_parentExperiment.ProteinStates.Add(this);
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
experiment = new Experiment("testExperiment1", new ProjectBase("testProject1", @"..\..\..\..\testData\testProjects\"), new HydraExperimentType(mockServiceLocator.Object));
DeleteTestResultFile();
}
public static IList<Result> OpenDirectory(Experiment experiment)
{
string[] resultFiles = Directory.GetFiles(Path.Combine(GetFullPath(experiment)), "*.xml");
IList<Result> results = new List<Result>();
foreach (string resultFile in resultFiles)
{
results.Add(Result.Open(experiment, Path.GetFileName(resultFile)));
}
return results;
}
public void TestInitialize()
{
ProjectBase project = TestHelper.CreateTestProject();
experiment = project.Experiments.First() as Experiment;
viewModel = new ExperimentViewModel(experiment);
}
