/// <summary>
/// Process Analysis Job Items according to their individual file types
/// </summary>
/// <param name="analysisJobItems">Analysis Job Items</param>
/// <param name="bWorker"></param>
/// <returns>Processed Analysis Job Items</returns>
public IEnumerable <AnalysisJobItem> Process(IEnumerable <AnalysisJobItem> analysisJobItems, BackgroundWorker bWorker)
{
// analysisJobItems should have LcmsDataSet field be null
m_abortRequested = false;
m_currentItem = 0;
m_totalItems = analysisJobItems.Count();
foreach (var jobItem in analysisJobItems)
{
if (bWorker.CancellationPending || m_abortRequested)
{
break;
}
OnProgressChanged(new MtdbProgressChangedEventArgs(m_currentItem, m_totalItems, jobItem));
m_currentJob = jobItem;
m_analysisReader = PhrpReaderFactory.Create(jobItem.FilePath, ProcessorOptions);
m_analysisReader.ProgressChanged += analysisReader_ProgressChanged;
// Reads the jobItem using the reader returned by the Reader Factory
jobItem.DataSet = m_analysisReader.Read(jobItem.FilePath);
m_currentItem++;
}
return(analysisJobItems);
}
/// <summary>
/// Entry point for creating an LCMS Dataset using the PHRP Reader.
/// </summary>
/// <remarks>
/// If the path ends with "msgfplus.mzid" or "mzid.gz" then it's an MZIdentML file, but if it's not, then
/// it determines the type of reader to return based on the extension of the file, using that to
/// determine if it is a Sequest, XTandem, MSAlign or MSGF+ file
/// The if statement is due to the PHRP Reader not meaning to be used on .mzid files
/// </remarks>
/// <param name="path">File to be read</param>
/// <param name="options">Reader options</param>
/// <returns>An appropriate reader for the file</returns>
public static PHRPReaderBase Create(string path, Options options)
{
PHRPReaderBase reader = null;
var resultType = clsPHRPReader.AutoDetermineResultType(path);
if (path.EndsWith("mzid") || path.EndsWith("mzid.gz"))
{
reader = new MzIdentMlReader(options);
return(reader);
}
switch (resultType)
{
case clsPHRPReader.ePeptideHitResultType.XTandem:
reader = new XTandemPhrpReader(options);
break;
case clsPHRPReader.ePeptideHitResultType.Sequest:
reader = new SequestPhrpReader(options);
break;
case clsPHRPReader.ePeptideHitResultType.MSGFDB:
reader = new MsgfPlusPhrpReader(options);
break;
case clsPHRPReader.ePeptideHitResultType.MSAlign:
reader = new MsAlignPhrpReader(options);
break;
default:
//Unsupported format!! Oh no!!
reader = null;
break;
}
return(reader);
}
