private static void Main(string[] args)
{
var osVersionInfo = new clsOSVersionInfo();
if (osVersionInfo.GetOSVersion().ToLower().Contains("windows"))
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
}
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return;
}
// initialize parameters
var paramDic = new Dictionary <string, string>
{
{ "-s", null },
{ "-d", null },
{ "-o", null },
{ "-e", "1" },
{ "-ntt", "2" },
{ "-mod", null },
{ "-t", "10" },
{ "-f", "10" },
{ "-tda", "0" },
{ "-minLength", "6" },
{ "-maxLength", "40" },
{ "-minCharge", "1" },
{ "-maxCharge", "4" },
{ "-minFragCharge", "1" },
{ "-maxFragCharge", "3" }
};
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;
}
paramDic[key] = value;
}
var parameters = new BottomUpInputParameters();
var message = parameters.Parse(paramDic);
if (message != null)
{
PrintUsageInfo(message);
return;
}
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.Write();
foreach (var specFilePath in parameters.SpecFilePaths)
{
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
parameters.DatabaseFilePath,
parameters.OutputDir,
parameters.AminoAcidSet,
parameters.Enzyme)
{
MinSequenceLength = parameters.MinSequenceLength,
MaxSequenceLength = parameters.MaxSequenceLength,
MinPrecursorIonCharge = parameters.MinPrecursorIonCharge,
MaxPrecursorIonCharge = parameters.MaxPrecursorIonCharge,
MinProductIonCharge = parameters.MinProductIonCharge,
MaxProductIonCharge = parameters.MaxProductIonCharge,
PrecursorIonTolerancePpm = parameters.PrecursorIonTolerancePpm,
ProductIonTolerancePpm = parameters.ProductIonTolerancePpm,
//RunTargetDecoyAnalysisBool = parameters.TdaBool,
RunTargetDecoyAnalysis = parameters.Tda,
NumTolerableTermini = parameters.NumTolerableTermini,
};
bottomUpLauncher.RunSearch(CorrThreshold);
}
}
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
}
static int Main(string[] args)
{
LcMsFeatureFinderInputParameters parameters;
try
{
var osVersionInfo = new clsOSVersionInfo();
if (osVersionInfo.GetOSVersion().ToLower().Contains("windows"))
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
}
//args = new string[] {"-i", @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf", "-minMass", "3000", "-maxMass", "30000"};
var parser = new CommandLineParser <ProMexInputParameters>(Name, Version);
parser.UsageExamples.Add("To create a PNG of the features in an existing ms1ft file " +
"(requires both a .pbf file and a .ms1ft file):\n\tProMex.exe -i dataset.pbf -ms1ft dataset.ms1ft -featureMap");
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);
}
parameters = results.ParsedResults;
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
{
#endif
// Example text: ProMex version 1.0.6527 (November 14, 2017)
// (the build date is computed automatically)
Console.WriteLine("************ {0} {1} ************", Name, Version);
parameters.Display();
var launcher = new LcMsFeatureFinderLauncher(parameters);
int errorCode;
if (string.IsNullOrWhiteSpace(parameters.ExistingFeaturesFilePath))
{
errorCode = launcher.Run();
}
else
{
errorCode = launcher.CreateFeatureMapImage(parameters.InputPath, parameters.ExistingFeaturesFilePath);
}
return(errorCode);
#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);
}
return(errorCode);
}
#endif
}
public static int Main(string[] args)
{
var errorCode = 0;
#if (!DEBUG)
try
#endif
{
var osVersionInfo = new clsOSVersionInfo();
if (osVersionInfo.GetOSVersion().ToLower().Contains("windows"))
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
}
string entryAsmName;
try
{
entryAsmName = System.Reflection.Assembly.GetEntryAssembly().GetName().Name;
}
catch
{
// This method was likely invoked by NUnit
entryAsmName = "Unknown_Assembly";
}
var parser = new CommandLineParser <TopDownInputParameters>(entryAsmName, Version);
parser.UsageExamples.Add(string.Format("Perform a target+decoy search with default parameters and a mods file:\n{0}.exe -s testfile.raw -d sampleProteins.fasta -mod mods.txt -tda 1", entryAsmName));
// TODO: add more examples, maybe a link to GitHub?
var results = parser.ParseArgs(args);
if (!results.Success)
{
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-3);
}
if (!results.ParsedResults.Validate())
{
parser.PrintHelp();
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-3);
}
var parameters = results.ParsedResults;
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.MaxNumNTermCleavages = 1; // max number of N-term cleavages
parameters.MaxNumCTermCleavages = 0; // max number of C-term cleavages
foreach (var specFilePath in parameters.SpecFilePaths)
{
// Update the spec file path in the parameters for each search
parameters.SpecFilePath = specFilePath;
parameters.Write();
var topDownLauncher = new IcTopDownLauncher(parameters);
topDownLauncher.ErrorEvent += TopDownLauncher_ErrorEvent;
topDownLauncher.WarningEvent += TopDownLauncher_WarningEvent;
topDownLauncher.StatusEvent += TopDownLauncher_StatusEvent;
topDownLauncher.ProgressUpdate += TopDownLauncher_ProgressUpdate;
var success = topDownLauncher.RunSearch();
if (success)
{
continue;
}
// topDownLauncher returned false (not successful)
// NOTE: The DMS Analysis Manager looks for this text; do not change it
var errorMsg = "Error processing " + Path.GetFileName(specFilePath) + ": ";
if (string.IsNullOrWhiteSpace(topDownLauncher.ErrorMessage))
{
errorMsg += "unknown error";
}
else
{
errorMsg += topDownLauncher.ErrorMessage;
}
Console.WriteLine(errorMsg);
if (errorCode == 0)
{
// This is the first error encountered; update the error code
// (though we will continue processing the next file if there is one)
errorCode = -Math.Abs(errorMsg.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
}
}
#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);
errorCode = -Math.Abs(ex.Message.GetHashCode());
System.Threading.Thread.Sleep(1500);
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
#endif
return(errorCode);
}
