/// <summary>
/// Configure and call the protein mapper
/// </summary>
/// <returns></returns>
private bool MapProteins()
{
// Configure the peptide to protein mapper
var options = new ProteinCoverageSummarizerOptions
{
IgnoreILDifferences = false,
MatchPeptidePrefixAndSuffixToProtein = false,
OutputProteinSequence = false,
PeptideFileSkipFirstLine = false,
RemoveSymbolCharacters = true,
ProteinInputFilePath = mFastaFilePath,
SaveProteinToPeptideMappingFile = true,
SearchAllProteinsForPeptideSequence = true,
SearchAllProteinsSkipCoverageComputationSteps = true
};
var peptideToProteinMapper = new clsPeptideToProteinMapEngine(options)
{
DeleteTempFiles = true,
InspectParameterFilePath = string.Empty,
PeptideInputFileFormat = clsPeptideToProteinMapEngine.PeptideInputFileFormatConstants.PeptideListFile,
};
if (!string.IsNullOrEmpty(mOutputDirectoryPath))
{
peptideToProteinMapper.LogMessagesToFile = true;
peptideToProteinMapper.LogDirectoryPath = mOutputDirectoryPath;
peptideToProteinMapper.LogFilePath = "PeptideToProteinMapper_Log.txt";
}
else
{
peptideToProteinMapper.LogMessagesToFile = false;
}
peptideToProteinMapper.ProgressUpdate += PeptideToProteinMapper_ProgressUpdate;
// Note that clsPeptideToProteinMapEngine utilizes Data.SQLite.dll
var success = peptideToProteinMapper.ProcessFile(mPeptideListFilePath, mOutputDirectoryPath, string.Empty, true);
peptideToProteinMapper.CloseLogFileNow();
return(success);
}
public static int Main()
{
// Returns 0 if no error, error code if an error
int returnCode;
var commandLineParser = new clsParseCommandLine();
bool proceed;
returnCode = 0;
mPeptideInputFilePath = string.Empty;
mProteinInputFilePath = string.Empty;
mParameterFilePath = string.Empty;
mInspectParameterFilePath = string.Empty;
mIgnoreILDifferences = false;
mOutputProteinSequence = true;
mSaveProteinToPeptideMappingFile = true;
mSaveSourceDataPlusProteinsFile = false;
mSkipCoverageComputationSteps = false;
mInputFileFormatCode = clsPeptideToProteinMapEngine.ePeptideInputFileFormatConstants.AutoDetermine;
mLogMessagesToFile = false;
mLogFilePath = string.Empty;
mLogDirectoryPath = string.Empty;
try
{
proceed = false;
if (commandLineParser.ParseCommandLine())
{
if (SetOptionsUsingCommandLineParameters(commandLineParser))
{
proceed = true;
}
}
if (!proceed || commandLineParser.NeedToShowHelp || commandLineParser.ParameterCount + commandLineParser.NonSwitchParameterCount == 0)
{
ShowProgramHelp();
returnCode = -1;
}
else
{
try
{
if (mVerboseLogging)
{
CreateVerboseLogFile();
}
if (string.IsNullOrWhiteSpace(mPeptideInputFilePath))
{
ShowErrorMessage("Peptide input file must be defined via /I (or by listing the filename just after the .exe)");
returnCode = -1;
return(returnCode);
}
else if (string.IsNullOrWhiteSpace(mProteinInputFilePath))
{
ShowErrorMessage("Protein input file must be defined via /R");
returnCode = -1;
return(returnCode);
}
mPeptideToProteinMapEngine = new clsPeptideToProteinMapEngine()
{
ProteinInputFilePath = mProteinInputFilePath,
LogMessagesToFile = mLogMessagesToFile,
LogFilePath = mLogFilePath,
LogDirectoryPath = mLogDirectoryPath,
PeptideInputFileFormat = mInputFileFormatCode,
InspectParameterFilePath = mInspectParameterFilePath,
IgnoreILDifferences = mIgnoreILDifferences,
OutputProteinSequence = mOutputProteinSequence,
SaveProteinToPeptideMappingFile = mSaveProteinToPeptideMappingFile,
SaveSourceDataPlusProteinsFile = mSaveSourceDataPlusProteinsFile,
SearchAllProteinsSkipCoverageComputationSteps = mSkipCoverageComputationSteps
};
mPeptideToProteinMapEngine.StatusEvent += PeptideToProteinMapEngine_StatusEvent;
mPeptideToProteinMapEngine.ErrorEvent += PeptideToProteinMapEngine_ErrorEvent;
mPeptideToProteinMapEngine.WarningEvent += PeptideToProteinMapEngine_WarningEvent;
mPeptideToProteinMapEngine.ProgressUpdate += PeptideToProteinMapEngine_ProgressChanged;
mPeptideToProteinMapEngine.ProgressReset += PeptideToProteinMapEngine_ProgressReset;
mPeptideToProteinMapEngine.ProcessFilesWildcard(mPeptideInputFilePath, mOutputDirectoryPath, mParameterFilePath);
if (mVerboseLogFile != null)
{
mVerboseLogFile.Close();
}
}
catch (Exception ex)
{
ShowErrorMessage("Error initializing the Peptide to Protein Mapper Options " + ex.Message);
}
}
}
catch (Exception ex)
{
ShowErrorMessage("Error occurred in modMain->Main: " + Environment.NewLine + ex.Message);
returnCode = -1;
}
return(returnCode);
}