/// <summary>
/// Constructor
/// </summary>
/// <param name="inputDirectoryPath">Input directory path</param>
/// <param name="resultToSeqMapFilename">ResultToSeqMap filename</param>
/// <param name="seqToProteinMapFilename"></param>
/// <param name="seqInfoFilename">SeqInfo filename</param>
public PHRPSeqMapReader(string inputDirectoryPath, string resultToSeqMapFilename, string seqToProteinMapFilename, string seqInfoFilename)
{
InputDirectoryPath = inputDirectoryPath;
if (string.IsNullOrEmpty(InputDirectoryPath))
{
InputDirectoryPath = string.Empty;
}
PeptideHitResultType = ReaderFactory.AutoDetermineResultType(resultToSeqMapFilename);
if (PeptideHitResultType == PeptideHitResultTypes.Unknown)
{
ErrorMessage = "Unable to auto-determine the PeptideHit result type based on filename " + resultToSeqMapFilename;
throw new Exception(ErrorMessage);
}
DatasetName = ReaderFactory.AutoDetermineDatasetName(resultToSeqMapFilename);
if (string.IsNullOrEmpty(DatasetName))
{
ErrorMessage = "Unable to auto-determine the dataset name using filename '" + resultToSeqMapFilename + "'";
throw new Exception(ErrorMessage);
}
ResultToSeqMapFilename = resultToSeqMapFilename;
SeqToProteinMapFilename = seqToProteinMapFilename;
mSeqInfoFilename = seqInfoFilename;
MaxProteinsPerSeqID = 0;
}
protected bool InitializeReader(FileInfo inputFile)
{
try
{
var peptideHitResultType = ReaderFactory.AutoDetermineResultType(inputFile.FullName);
if (peptideHitResultType == PeptideHitResultTypes.Unknown)
{
OnErrorEvent("Error: Could not determine the format of the PHRP data file: " + inputFile.FullName);
return(false);
}
// Open the data file and read the data
mPHRPReader = new ReaderFactory(inputFile.FullName, PeptideHitResultTypes.Unknown, false, false, false)
{
EchoMessagesToConsole = false,
SkipDuplicatePSMs = false
};
if (!mPHRPReader.CanRead)
{
OnErrorEvent("Aborting since PHRPReader is not ready: " + mPHRPReader.ErrorMessage);
return(false);
}
// Attach the events
RegisterEvents(mPHRPReader);
}
catch (Exception ex)
{
OnErrorEvent("Error in InitializeReader: " + ex.Message);
return(false);
}
return(true);
}
public static PeptideHitResultTypes AutoDetermineResultType(string filePath)
{
return(ReaderFactory.AutoDetermineResultType(filePath));
}