/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return reader;
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return(reader);
}
public void TestLoadingProteoWizardWrapper()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//try
//{
var reader = new ProteoWizardReader(TestRawFilePath);
reader.ReadMassSpectrum(1);
//}
//catch (FileNotFoundException e)
//{
// Console.WriteLine("FileNotFound: {0}", e.FileName);
//}
//var mzs = new[] {1.0};
//var intensities = new[] {10000.0};
//var centroider = new Centroider(mzs, intensities);
//centroider.GetCentroidedData(out mzs, out intensities);
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.DeconvolutedPbfFile:
reader = new DPbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
else
{
ConsoleMsgUtils.ShowWarning(string.Format("WARNING: Could not find a reader for file \"{0}\"." +
" Is MSFileReader and/or ProteoWizard installed?", filePath));
}
break;
}
return(reader);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="filePath"></param>
/// <remarks>To avoid assembly resolving errors, the ProteoWizardAssemblyResolver should be added as an AssemblyResolve event handler, as follows:
/// <code>AppDomain.CurrentDomain.AssemblyResolve += ProteoWizardReader.ProteoWizardAssemblyResolver;</code>
/// </remarks>
public ProteoWizardReaderImplementation(string filePath)
{
AppDomain.CurrentDomain.AssemblyResolve += ProteoWizardAssemblyResolver;
FilePath = ProteoWizardReader.CheckForDirectoryDataset(filePath);
}
/// <summary>
/// Get the normalized dataset path; only returns a different string when the given path is to a file/folder in a folder-type dataset
/// </summary>
/// <param name="path"></param>
/// <returns>Normalized dataset path</returns>
public static string NormalizeDatasetPath(string path)
{
return(ProteoWizardReader.CheckForDirectoryDataset(path));
}
/// <summary>
/// Utility function: Gets the actual dataset name, needed in cases when a file in a folder-type dataset is given.
/// </summary>
/// <param name="path"></param>
/// <returns>The path to the dataset, or the path to the dataset directory</returns>
public static string GetDatasetName(string path)
{
return(ProteoWizardReader.CheckForDirectoryDataset(path));
}