public void CopyToScanner(clsMSFileInfoScanner scanner)
{
// Note: These values will be overridden if /P was used and they are defined in the parameter file
scanner.UseCacheFiles = UseCacheFiles;
scanner.ReprocessExistingFiles = ReprocessingExistingFiles;
scanner.ReprocessIfCachedSizeIsZero = ReprocessIfCachedSizeIsZero;
scanner.PlotWithPython = PlotWithPython;
scanner.SaveTICAndBPIPlots = SaveTICAndBPIPlots;
scanner.SaveLCMS2DPlots = SaveLCMS2DPlots;
scanner.LCMS2DPlotMaxPointsToPlot = LCMS2DMaxPointsToPlot;
scanner.LCMS2DOverviewPlotDivisor = LCMS2DOverviewPlotDivisor;
scanner.TestLCMSGradientColorSchemes = TestLCMSGradientColorSchemes;
scanner.CheckCentroidingStatus = CheckCentroidingStatus;
scanner.MS2MzMin = MS2MzMin;
scanner.DisableInstrumentHash = DisableInstrumentHash;
scanner.ScanStart = ScanStart;
scanner.ScanEnd = ScanEnd;
scanner.ShowDebugInfo = ShowDebugInfo;
scanner.ComputeOverallQualityScores = ComputeOverallQualityScores;
scanner.CreateDatasetInfoFile = CreateDatasetInfoFile;
scanner.CreateScanStatsFile = CreateScanStatsFile;
scanner.UpdateDatasetStatsTextFile = UpdateDatasetStatsTextFile;
scanner.DatasetStatsTextFileName = DatasetStatsTextFileName;
scanner.CheckFileIntegrity = CheckFileIntegrity;
scanner.RecheckFileIntegrityForExistingDirectories = ReprocessingExistingFiles;
scanner.MaximumTextFileLinesToCheck = MaximumTextFileLinesToCheck;
scanner.ComputeFileHashes = ComputeFileHashes;
scanner.ZipFileCheckAllData = ZipFileCheckAllData;
scanner.IgnoreErrorsWhenRecursing = IgnoreErrorsWhenRecursing;
if (LogFilePath.Length > 0)
{
scanner.LogMessagesToFile = true;
scanner.LogFilePath = LogFilePath;
}
scanner.DatasetIDOverride = DatasetID;
scanner.DSInfoDBPostingEnabled = PostResultsToDMS;
if (!string.IsNullOrEmpty(ParameterFilePath))
{
scanner.LoadParameterFileSettings(ParameterFilePath);
}
}
public static int Main()
{
int intReturnCode;
var objParseCommandLine = new clsParseCommandLine();
mInputDataFilePath = string.Empty;
mOutputFolderName = string.Empty;
mParameterFilePath = string.Empty;
mLogFilePath = string.Empty;
mRecurseFolders = false;
mRecurseFoldersMaxLevels = 2;
mIgnoreErrorsWhenRecursing = false;
mReprocessingExistingFiles = false;
mReprocessIfCachedSizeIsZero = false;
mUseCacheFiles = false;
mSaveTICandBPIPlots = true;
mSaveLCMS2DPlots = false;
mLCMS2DMaxPointsToPlot = clsLCMSDataPlotterOptions.DEFAULT_MAX_POINTS_TO_PLOT;
mLCMS2DOverviewPlotDivisor = clsLCMSDataPlotterOptions.DEFAULT_LCMS2D_OVERVIEW_PLOT_DIVISOR;
mTestLCMSGradientColorSchemes = false;
mCheckCentroidingStatus = false;
mScanStart = 0;
mScanEnd = 0;
mShowDebugInfo = false;
mComputeOverallQualityScores = false;
mCreateDatasetInfoFile = false;
mCreateScanStatsFile = false;
mUpdateDatasetStatsTextFile = false;
mDatasetStatsTextFileName = string.Empty;
mCheckFileIntegrity = false;
mComputeFileHashes = false;
mZipFileCheckAllData = true;
mMaximumTextFileLinesToCheck = clsFileIntegrityChecker.DEFAULT_MAXIMUM_TEXT_FILE_LINES_TO_CHECK;
mPostResultsToDMS = false;
mPlotWithPython = false;
mLastProgressTime = DateTime.UtcNow;
try
{
var blnProceed = false;
if (objParseCommandLine.ParseCommandLine())
{
if (SetOptionsUsingCommandLineParameters(objParseCommandLine))
{
blnProceed = true;
}
}
if (mInputDataFilePath == null)
{
mInputDataFilePath = string.Empty;
}
if (!blnProceed || objParseCommandLine.NeedToShowHelp || objParseCommandLine.ParameterCount + objParseCommandLine.NonSwitchParameterCount == 0 || mInputDataFilePath.Length == 0)
{
ShowProgramHelp();
return(-1);
}
var scanner = new clsMSFileInfoScanner();
scanner.DebugEvent += mMSFileScanner_DebugEvent;
scanner.ErrorEvent += mMSFileScanner_ErrorEvent;
scanner.WarningEvent += mMSFileScanner_WarningEvent;
scanner.StatusEvent += mMSFileScanner_MessageEvent;
scanner.ProgressUpdate += mMSFileScanner_ProgressUpdate;
if (mCheckFileIntegrity)
{
mUseCacheFiles = true;
}
// Note: These values will be overridden if /P was used and they are defined in the parameter file
scanner.UseCacheFiles = mUseCacheFiles;
scanner.ReprocessExistingFiles = mReprocessingExistingFiles;
scanner.ReprocessIfCachedSizeIsZero = mReprocessIfCachedSizeIsZero;
scanner.PlotWithPython = mPlotWithPython;
scanner.SaveTICAndBPIPlots = mSaveTICandBPIPlots;
scanner.SaveLCMS2DPlots = mSaveLCMS2DPlots;
scanner.LCMS2DPlotMaxPointsToPlot = mLCMS2DMaxPointsToPlot;
scanner.LCMS2DOverviewPlotDivisor = mLCMS2DOverviewPlotDivisor;
scanner.TestLCMSGradientColorSchemes = mTestLCMSGradientColorSchemes;
scanner.CheckCentroidingStatus = mCheckCentroidingStatus;
scanner.ScanStart = mScanStart;
scanner.ScanEnd = mScanEnd;
scanner.ShowDebugInfo = mShowDebugInfo;
scanner.ComputeOverallQualityScores = mComputeOverallQualityScores;
scanner.CreateDatasetInfoFile = mCreateDatasetInfoFile;
scanner.CreateScanStatsFile = mCreateScanStatsFile;
scanner.UpdateDatasetStatsTextFile = mUpdateDatasetStatsTextFile;
scanner.DatasetStatsTextFileName = mDatasetStatsTextFileName;
scanner.CheckFileIntegrity = mCheckFileIntegrity;
scanner.MaximumTextFileLinesToCheck = mMaximumTextFileLinesToCheck;
scanner.ComputeFileHashes = mComputeFileHashes;
scanner.ZipFileCheckAllData = mZipFileCheckAllData;
scanner.IgnoreErrorsWhenRecursing = mIgnoreErrorsWhenRecursing;
if (mLogFilePath.Length > 0)
{
scanner.LogMessagesToFile = true;
scanner.LogFilePath = mLogFilePath;
}
scanner.DatasetIDOverride = mDatasetID;
scanner.DSInfoDBPostingEnabled = mPostResultsToDMS;
if (!string.IsNullOrEmpty(mParameterFilePath))
{
scanner.LoadParameterFileSettings(mParameterFilePath);
}
if (mRecurseFolders)
{
if (scanner.ProcessMSFilesAndRecurseFolders(mInputDataFilePath, mOutputFolderName, mRecurseFoldersMaxLevels))
{
intReturnCode = 0;
}
else
{
intReturnCode = (int)scanner.ErrorCode;
}
}
else
{
if (scanner.ProcessMSFileOrFolderWildcard(mInputDataFilePath, mOutputFolderName, true))
{
intReturnCode = 0;
}
else
{
intReturnCode = (int)scanner.ErrorCode;
if (intReturnCode != 0)
{
ShowErrorMessage("Error while processing: " + scanner.GetErrorMessage());
}
}
}
scanner.SaveCachedResults();
}
catch (Exception ex)
{
ShowErrorMessage("Error occurred in modMain->Main: " + Environment.NewLine + ex.Message);
intReturnCode = -1;
}
return(intReturnCode);
}