public static ProjectBase CreateTestProject()
{
DeleteProjectDirectory();
Mock<IEventAggregator> mockEventAggregator = new Mock<IEventAggregator>();
Mock<IServiceLocator> mockServiceLocator = new Mock<IServiceLocator>();
mockServiceLocator.Setup(mock => mock.GetAllInstances<IDataProvider>()).Returns(new List<IDataProvider>() { new ProteoWizardDataProvider(mockEventAggregator.Object) });
ProjectBase project = new ProjectBase("temp", @"c:\");
HydraExperimentType hydraExperimentType = new HydraExperimentType(mockServiceLocator.Object);
Experiment experiment = hydraExperimentType.CreateExperiment(project, "testExperiment") as Experiment;
ProteinState proteinState1 = new ProteinState(experiment);
ProteinState proteinState2 = new ProteinState(experiment);
Labeling labeling1 = new Labeling(experiment);
Labeling labeling2 = new Labeling(experiment);
CreateRun(Properties.Settings.Default.mzXMLTestFile1, proteinState1, labeling1, experiment, mockEventAggregator);
CreateRun(Properties.Settings.Default.mzXMLTestFile2, proteinState1, labeling1, experiment, mockEventAggregator);
CreateRun(Properties.Settings.Default.mzXMLTestFile2, proteinState1, labeling2, experiment, mockEventAggregator);
CreateRun(Properties.Settings.Default.mzXMLTestFile2, proteinState2, labeling1, experiment, mockEventAggregator);
experiment.Peptides.PeptideCollection.Add(CreatePeptide("SAMPLE", 1));
experiment.Peptides.PeptideCollection.Add(CreatePeptide("SAMPLES", 20));
experiment.Save();
project.Experiments.Add(experiment);
return project;
}
public DeuterationResult(Peptide peptide, ProteinState proteinState, Labeling labeling, IList<RunResult> replicateResults)
{
_peptide = peptide;
_proteinState = proteinState;
_labeling = labeling;
_replicateResults = replicateResults;
DeuterationValues = new List<double>();
DeuterationDistributedDeuterationValues = new List<double>();
CentroidMassValues = new List<double>();
NValue = 0;
foreach (RunResult replicate in _replicateResults)
{
if (replicate != null)
{
this.TheoreticalCentroidMass = replicate.TheoreticalAverageMass;
if (replicate.IsUsedInCalculations)
{
DeuterationValues.Add(replicate.AmountDeut);
DeuterationDistributedDeuterationValues.Add(replicate.AmountDeutFromDeutDist);
CentroidMassValues.Add(replicate.AverageMass);
NValue++;
}
}
}
}
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 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 void NotEqualOperator()
{
ProteinState proteinState2 = new ProteinState(experiment);
Assert.IsTrue(proteinState != proteinState2);
proteinState2.Name = "Protein state 1";
Assert.IsFalse(proteinState != proteinState2);
}
public void Equals()
{
ProteinState proteinState2 = new ProteinState(experiment);
Assert.IsFalse(proteinState.Equals(proteinState2));
proteinState2.Name = "Protein state 1";
Assert.IsTrue(proteinState.Equals(proteinState2));
}
public ProteinStateDeuterationResult(IList<RunResult> replicates, ProteinState proteinState)
: this()
{
_replicateResults = replicates;
_proteinState = proteinState;
foreach (RunResult rr in this.ReplicateResults)
{
if (rr != null)
{
this.TheoreticalCentroidMass = rr.TheoreticalAverageMass;
if (rr.IsUsedInCalculations)
{
DeuterationValues.Add(rr.AmountDeut);
DeuterationDistributedDeuterationValues.Add(rr.AmountDeutFromDeutDist);
CentroidMassValues.Add(rr.AverageMass);
}
}
}
this.NValue = DeuterationValues.Count;
}
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;
}
private Experiment CreateTestExperiment()
{
Experiment experiment = hydraExperimentType.CreateExperiment(project, TestExperimentName) as Experiment;
ProteinState proteinState = new ProteinState(experiment);
Labeling labeling = new Labeling(experiment);
string runFileName = Path.GetFileName(Properties.Settings.Default.mzXMLTestFile1);
File.Copy(Properties.Settings.Default.mzXMLTestFile1, Path.Combine(TestExperimentDirectory, "Data", runFileName), true);
Run run = new Run(
@"Data\" + runFileName,
Path.Combine(TestExperimentDirectory, "Data", runFileName),
proteinState,
labeling,
experiment,
new ProteoWizardDataProvider(mockEventAggregator.Object));
experiment.Save();
return experiment as Experiment;
}
public IList<Run> GetRunsByProteinState(ProteinState proteinState)
{
return (from data in Runs
where data.ProteinState == proteinState
select data).ToList();
}
public void TestInitialize()
{
mockServiceLocator = new Mock<IServiceLocator>();
experiment = TestHelper.GetTestExperiment(mockServiceLocator);
proteinState = new ProteinState(experiment);
}
public void GetNextName()
{
Assert.AreEqual("Protein state 1", proteinState.Name);
ProteinState proteinState2 = new ProteinState(experiment);
Assert.AreEqual("Protein state 2", proteinState2.Name);
}
public void Save()
{
OpenExperiment();
Assert.AreEqual(2, experiment.ProteinStates.Count);
ProteinState proteinState = new ProteinState(experiment);
experiment.Save();
OpenExperiment();
Assert.AreEqual(3, experiment.ProteinStates.Count);
experiment.ProteinStates.Remove(experiment.ProteinStates[2]);
experiment.Save();
}
