/// <summary>
/// Initializes a new instance of the <see cref="LibraryMatchWorkflow"/> class.
/// </summary>
/// <param name="uimfFileLocation">
/// The UIMF file location.
/// </param>
/// <param name="outputDirectory">
/// The output directory.
/// </param>
/// <param name="resultFileName">
/// The result file name.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public LibraryMatchWorkflow(string uimfFileLocation, string outputDirectory, string resultFileName, LibraryMatchParameters parameters)
{
this.uimfReader = new DataReader(uimfFileLocation);
// Append bin-centric table to the uimf if not present.
if (!this.uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
this.Parameters = parameters;
this.smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
this.NumberOfFrames = this.uimfReader.GetGlobalParams().NumFrames;
this.NumberOfScans = this.uimfReader.GetFrameParams(1).Scans;
this.DatasetName = Path.GetFileNameWithoutExtension(uimfFileLocation);
this.Parameters = parameters;
this.ResultFileName = resultFileName;
if (outputDirectory == string.Empty)
{
outputDirectory = Directory.GetCurrentDirectory();
}
if (!outputDirectory.EndsWith("\\"))
{
outputDirectory += "\\";
}
if (!Directory.Exists(outputDirectory))
{
try
{
Directory.CreateDirectory(outputDirectory);
}
catch (Exception)
{
Console.WriteLine("Failed to create directory.");
throw;
}
}
this.OutputPath = outputDirectory;
Trace.Listeners.Clear();
ConsoleTraceListener consoleTraceListener = new ConsoleTraceListener(false);
consoleTraceListener.TraceOutputOptions = TraceOptions.DateTime;
string result = this.OutputPath + this.ResultFileName;
this.resultFileWriter = File.AppendText(result);
TextWriterTraceListener resultFileTraceListener = new TextWriterTraceListener(this.resultFileWriter)
{
Name = "this.DatasetName" + "_Result",
TraceOutputOptions = TraceOptions.ThreadId | TraceOptions.DateTime
};
Trace.Listeners.Add(consoleTraceListener);
Trace.Listeners.Add(resultFileTraceListener);
Trace.AutoFlush = true;
}
/// <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;
}
