public void TestMixedSampleLibraryMatching()
{
// TODO Import AMT library instead of manually add them
IList<DriftTimeTarget> imsTargets = new List<DriftTimeTarget>();
DriftTimeTarget t1 = new DriftTimeTarget("BPS protonated", 23.22, "C12H10O4S", IonizationMethod.Protonated);
DriftTimeTarget t2 = new DriftTimeTarget("BPS sodiated", 31.8506, "C12H10O4S", IonizationMethod.Sodiumated);
DriftTimeTarget t3 = new DriftTimeTarget("I made it up", 15, "C14H14O4S", IonizationMethod.Sodiumated);
DriftTimeTarget t4 = new DriftTimeTarget("I made it up again", 15, "C12H11O4S", IonizationMethod.Sodiumated);
imsTargets.Add(t3);
imsTargets.Add(t1);
imsTargets.Add(t2);
imsTargets.Add(t4);
LibraryMatchWorkflow workflow = new LibraryMatchWorkflow(BPSPostive, "output", "result.txt", new LibraryMatchParameters());
IDictionary<DriftTimeTarget, LibraryMatchResult> results = workflow.RunLibraryMatchWorkflow(imsTargets);
Assert.AreEqual(results[t1].AnalysisStatus, AnalysisStatus.Positive);
Assert.AreEqual(results[t2].AnalysisStatus, AnalysisStatus.Positive);
Assert.AreEqual(results[t3].AnalysisStatus, AnalysisStatus.Negative);
Assert.AreEqual(results[t4].AnalysisStatus, AnalysisStatus.Negative);
}
/// <summary>
/// The execute match.
/// </summary>
/// <param name="options">
/// The options.
/// </param>
/// <returns>
/// The <see cref="int"/>.
/// </returns>
private static int ExecuteMatch(MatchOptions options)
{
string inputPath = options.InputPath; // get the UIMF file
string libraryPath = options.LibraryPath;
string datasetName = Path.GetFileNameWithoutExtension(inputPath);
string libraryFlieName = Path.GetFileNameWithoutExtension(libraryPath);
string resultName = datasetName + "_" + libraryFlieName + "_MatchResult.txt";
string resultPath = Path.Combine(options.OutputPath, resultName);
string outputDirectory = options.OutputPath;
if (outputDirectory == string.Empty)
{
outputDirectory = Directory.GetCurrentDirectory();
}
if (!Directory.Exists(outputDirectory))
{
try
{
Directory.CreateDirectory(outputDirectory);
}
catch (Exception)
{
Console.WriteLine(string.Format("Failed to create directory {0}", outputDirectory));
throw;
}
}
// Delete the result file if it already exists
if (File.Exists(resultPath))
{
File.Delete(resultPath);
}
IList<DriftTimeTarget> importDriftTimeLibrary = DriftTimeLibraryImporter.ImportDriftTimeLibrary(libraryPath);
var parameters = new LibraryMatchParameters(options.DriftTimeError, 250, 9, options.PeakShapeScoreThreshold, options.IsotopicScoreThreshold, 0.25, options.MassError, options.DriftTubeLength);
LibraryMatchWorkflow workflow = new LibraryMatchWorkflow(inputPath, outputDirectory, resultName, parameters);
IDictionary<DriftTimeTarget, LibraryMatchResult> results = workflow.RunLibraryMatchWorkflow(importDriftTimeLibrary);
// Write out the target / result pairs as serialized objects
if (options.PauseWhenDone)
{
PauseProgram();
}
return 1;
}
