public static int Main(string[] args)
{
PbfGenInputParameters options;
try
{
var osVersionInfo = new clsOSVersionInfo();
if (osVersionInfo.GetOSVersion().ToLower().Contains("windows"))
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
}
var exeName = System.Reflection.Assembly.GetEntryAssembly().GetName().Name;
var parser = new CommandLineParser <PbfGenInputParameters>(exeName, Version);
parser.UsageExamples.Add($"Using -start and -end to limit the scan range to include in the .pbf file\n\t{exeName}.exe -s Dataset.raw -start 2000 -end 3000");
var results = parser.ParseArgs(args);
if (!results.Success)
{
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-1);
}
if (!results.ParsedResults.Validate())
{
parser.PrintHelp();
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-1);
}
options = results.ParsedResults;
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
#endif
{
var specFilePaths = new[] { options.SourcePath };
if (Directory.Exists(options.SourcePath) && !MassSpecDataReaderFactory.IsADirectoryDataset(options.SourcePath))
{
specFilePaths = Directory.GetFiles(options.SourcePath, "*.raw"); // TODO: Support folders with other formats in them too...
}
foreach (var rawFilePath in specFilePaths)
{
var pbfFileName = MassSpecDataReaderFactory.ChangeExtension(rawFilePath, PbfLcMsRun.FileExtensionConst);
var pbfFilePath = Path.Combine(options.OutputDir, Path.GetFileName(pbfFileName));
if (File.Exists(pbfFilePath) && PbfLcMsRun.CheckFileFormatVersion(pbfFilePath, out var isCurrent) && isCurrent)
{
Console.WriteLine("{0} already exists.", pbfFilePath);
continue;
}
Console.WriteLine("Creating {0} from {1}", pbfFilePath, rawFilePath);
if (options.StartScan > 0 && options.EndScan > 0)
{
Console.WriteLine("Only including scans {0} to {1}", options.StartScan, options.EndScan);
}
else if (options.StartScan > 0)
{
Console.WriteLine("Only including scans {0} to the end", options.StartScan);
}
else if (options.EndScan > 0)
{
Console.WriteLine("Only including scans 1 to {0}", options.EndScan);
}
var reader = MassSpecDataReaderFactory.GetMassSpecDataReader(rawFilePath);
var progress = new Progress <ProgressData>(p =>
{
p.UpdateFrequencySeconds = 2;
if ((p.Percent % 25).Equals(0) || p.ShouldUpdate())
{
Console.Write("\r{0}, {1:00.0}% complete ", p.Status, p.Percent);
}
});
var run = new PbfLcMsRun(rawFilePath, reader, pbfFilePath, 0, 0, progress, false, options.StartScan, options.EndScan);
Console.WriteLine();
}
Console.WriteLine("PbfFormatVersion: {0}", PbfLcMsRun.FileFormatId);
return(0);
}
#if (!DEBUG)
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
var errorCode = -Math.Abs(ex.Message.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
#endif
}
public static int Main(string[] args)
{
string specFilePath;
string outputDir;
try
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
if (args.Length == 0)
{
PrintUsageInfo();
return(-1);
}
var paramDic = new Dictionary <string, string>
{
{ "-s", null },
{ "-o", null }
};
for (var i = 0; i < args.Length / 2; i++)
{
var key = args[2 * i];
var value = args[2 * i + 1];
if (!paramDic.ContainsKey(key))
{
PrintUsageInfo("Invalid parameter: " + key);
return(-1);
}
paramDic[key] = value;
}
// Parse command line parameters
specFilePath = paramDic["-s"];
if (specFilePath == null)
{
PrintUsageInfo("Missing required parameter -s!");
return(-1);
}
// Check for folder-type datasets, and replace specFilePath with the directory name if it is.
specFilePath = MassSpecDataReaderFactory.GetDatasetName(specFilePath);
var isDirectoryDataset = MassSpecDataReaderFactory.IsADirectoryDataset(specFilePath);
// True if specFilePath is a directory that is NOT a supported folder-type dataset.
var specPathIsDirectory = Directory.Exists(specFilePath) && !isDirectoryDataset;
if (!File.Exists(specFilePath) && !specPathIsDirectory && !isDirectoryDataset)
{
PrintUsageInfo("File not found: " + specFilePath);
return(-1);
}
var types = MassSpecDataReaderFactory.MassSpecDataTypeFilterList;
types.Remove(".pbf");
if (!specPathIsDirectory && !(types.Select(ext => specFilePath.ToLower().EndsWith(ext)).Any()))
{
PrintUsageInfo("Invalid file extension: (" + Path.GetExtension(specFilePath) + ") " + specFilePath);
return(-1);
}
// Must use "Path.GetFullPath" to return the absolute path when the source file is in the working directory
// But, it could cause problems with too-long paths.
outputDir = paramDic["-o"] ?? (specPathIsDirectory ? specFilePath : Path.GetDirectoryName(Path.GetFullPath(specFilePath)));
if (outputDir == null)
{
PrintUsageInfo("Invalid output file directory: " + specFilePath);
return(-1);
}
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
PrintUsageInfo("OutputDir " + outputDir + " is not a directory!");
return(-1);
}
Directory.CreateDirectory(outputDir);
}
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
{
#endif
string[] specFilePaths = new[] { specFilePath };
if (Directory.Exists(specFilePath) && !MassSpecDataReaderFactory.IsADirectoryDataset(specFilePath))
{
specFilePaths = Directory.GetFiles(specFilePath, "*.raw");
}
foreach (var rawFilePath in specFilePaths)
{
var pbfFilePath = Path.Combine(outputDir, Path.GetFileNameWithoutExtension(rawFilePath) + PbfLcMsRun.FileExtension);
bool isCurrent;
if (File.Exists(pbfFilePath) && PbfLcMsRun.CheckFileFormatVersion(pbfFilePath, out isCurrent) && isCurrent)
{
Console.WriteLine("{0} already exists.", pbfFilePath);
continue;
}
Console.WriteLine("Creating {0} from {1}", pbfFilePath, rawFilePath);
IMassSpecDataReader reader = MassSpecDataReaderFactory.GetMassSpecDataReader(rawFilePath);
var progress = new Progress <ProgressData>(p =>
{
p.UpdateFrequencySeconds = 2;
if ((p.Percent % 25).Equals(0) || p.ShouldUpdate())
{
Console.Write("\r{0}, {1:00.0}% complete ", p.Status, p.Percent);
}
});
var run = new PbfLcMsRun(rawFilePath, reader, pbfFilePath, 0, 0, progress);
Console.WriteLine();
}
Console.WriteLine("PbfFormatVersion: {0}", PbfLcMsRun.FileFormatId);
return(0);
#if (!DEBUG)
}
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
var errorCode = -Math.Abs(ex.Message.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
#endif
}
