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);
}
private static bool SetOptionsUsingCommandLineParameters(clsParseCommandLine CommandLineParser)
{
// Returns True if no problems; otherwise, returns false
// /I:PeptideInputFilePath /R: ProteinInputFilePath /O:OutputDirectoryPath /P:ParameterFilePath
string value = string.Empty;
var validParameters = new List <string>()
{
"I", "O", "R", "P", "F", "N", "G", "H", "K", "A", "L", "LogDir", "LogFolder", "VerboseLog"
};
int intValue;
try
{
// Make sure no invalid parameters are present
if (CommandLineParser.InvalidParametersPresent(validParameters))
{
ShowErrorMessage("Invalid command line parameters",
(from item in CommandLineParser.InvalidParameters(validParameters) select("/" + item)).ToList());
return(false);
}
else
{
// Query commandLineParser to see if various parameters are present
if (CommandLineParser.RetrieveValueForParameter("I", out value))
{
mPeptideInputFilePath = value;
}
else if (CommandLineParser.NonSwitchParameterCount > 0)
{
mPeptideInputFilePath = CommandLineParser.RetrieveNonSwitchParameter(0);
}
if (CommandLineParser.RetrieveValueForParameter("O", out value))
{
mOutputDirectoryPath = value;
}
if (CommandLineParser.RetrieveValueForParameter("R", out value))
{
mProteinInputFilePath = value;
}
if (CommandLineParser.RetrieveValueForParameter("P", out value))
{
mParameterFilePath = value;
}
if (CommandLineParser.RetrieveValueForParameter("F", out value))
{
if (int.TryParse(value, out intValue))
{
try
{
mInputFileFormatCode = (clsPeptideToProteinMapEngine.ePeptideInputFileFormatConstants)intValue;
}
catch (Exception ex)
{
// Conversion failed; leave mInputFileFormatCode unchanged
}
}
}
if (CommandLineParser.RetrieveValueForParameter("N", out value))
{
mInspectParameterFilePath = value;
}
if (CommandLineParser.RetrieveValueForParameter("G", out value))
{
mIgnoreILDifferences = true;
}
if (CommandLineParser.RetrieveValueForParameter("H", out value))
{
mOutputProteinSequence = false;
}
if (CommandLineParser.RetrieveValueForParameter("K", out value))
{
mSkipCoverageComputationSteps = true;
}
if (CommandLineParser.RetrieveValueForParameter("A", out value))
{
mSaveSourceDataPlusProteinsFile = true;
}
if (CommandLineParser.RetrieveValueForParameter("L", out value))
{
mLogMessagesToFile = true;
if (!string.IsNullOrEmpty(value))
{
mLogFilePath = value;
}
}
if (CommandLineParser.RetrieveValueForParameter("LogDir", out value))
{
mLogMessagesToFile = true;
if (!string.IsNullOrEmpty(value))
{
mLogDirectoryPath = value;
}
}
if (CommandLineParser.RetrieveValueForParameter("LogFolder", out value))
{
mLogMessagesToFile = true;
if (!string.IsNullOrEmpty(value))
{
mLogDirectoryPath = value;
}
}
if (CommandLineParser.RetrieveValueForParameter("VerboseLog", out value))
{
mVerboseLogging = true;
}
return(true);
}
}
catch (Exception ex)
{
ShowErrorMessage("Error parsing the command line parameters: " + Environment.NewLine + ex.Message);
}
return(false);
}
