static int Main(string[] args)
{
try
{
// Handles a bug in .NET console applications
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
// Get the version number
var assembly = Assembly.GetExecutingAssembly();
var assemblyVersion = assembly.GetName().Version.ToString();
Console.WriteLine("CrossLinkingIMS Console Application Version " + assemblyVersion);
var commandLineUtil = new CommandLineUtil(caseSensitiveSwitchNames: false);
// Make sure we have parameters. If not, then show the user the proper syntax
var doParametersExist = commandLineUtil.ParseCommandLine();
if (!doParametersExist)
{
ShowSyntax();
return -1;
}
// Get the Feature File Location
string featureFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("f", out featureFileLocation))
{
Console.WriteLine("-f switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(featureFileLocation))
{
return -4;
}
var featureFile = new FileInfo(featureFileLocation);
// Get the Peaks File Location
string peaksFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("p", out peaksFileLocation))
{
Console.WriteLine("-p switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(peaksFileLocation))
{
return -4;
}
var peaksFile = new FileInfo(peaksFileLocation);
// Get the FastA File Location
string fastAFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("fasta", out fastAFileLocation))
{
Console.WriteLine("-fasta switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(fastAFileLocation))
{
return -4;
}
var fastAFile = new FileInfo(fastAFileLocation);
// Get the PPM Mass Tolerance
string massToleranceString;
if (!commandLineUtil.RetrieveValueForParameter("ppm", out massToleranceString))
{
Console.WriteLine("-ppm switch is missing");
ShowSyntax();
return -2;
}
var massTolerance = double.Parse(massToleranceString);
// Get the Max Missed Cleavages
string maxMissedCleavagesString;
commandLineUtil.RetrieveValueForParameter("c", out maxMissedCleavagesString);
if (string.IsNullOrEmpty(maxMissedCleavagesString))
maxMissedCleavagesString = "1";
var maxMissedCleavages = int.Parse(maxMissedCleavagesString);
// Get the Partially Tryptic Flag
string trypticString;
commandLineUtil.RetrieveValueForParameter("t", out trypticString);
string staticDeltaMassString;
var staticDeltaMass = 0.0;
if (commandLineUtil.RetrieveValueForParameter("static", out staticDeltaMassString))
{
double.TryParse(staticDeltaMassString, out staticDeltaMass);
}
var useC13 = true;
var useN15 = true;
if (commandLineUtil.IsParameterPresent("c13off"))
useC13 = false;
if (commandLineUtil.IsParameterPresent("n15off"))
useN15 = false;
if (!(useC13 || useN15) && Math.Abs(staticDeltaMass) < float.Epsilon)
{
Console.WriteLine("If you use both -C13off and -N15off, you must use -Static:MassDiff to specify a static mass difference");
Thread.Sleep(1500);
return -3;
}
var settings = new CrossLinkSettings(massTolerance, maxMissedCleavages, trypticString, useC13, useN15, staticDeltaMass);
// Get the Output File Location
string outputFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("o", out outputFileLocation))
{
if (featureFile.DirectoryName != null && featureFile.DirectoryName == peaksFile.DirectoryName)
outputFileLocation = Path.Combine(featureFile.DirectoryName, "crossLinkResults.csv");
else
outputFileLocation = "crossLinkResults.csv";
}
// Run the cross-linking application
Console.WriteLine("Executing...");
var crossLinkResults = CrossLinkingImsController.Execute(settings, fastAFile, featureFile, peaksFile);
var outputFileInfo = new FileInfo(outputFileLocation);
// Output the results
Console.WriteLine("Outputting " + crossLinkResults.Count().ToString("#,##0") + " results to \n" + outputFileInfo.FullName);
CrossLinkUtil.OutputCrossLinkResults(crossLinkResults, outputFileInfo);
return 0;
}
catch (Exception ex)
{
Console.WriteLine();
Console.WriteLine("=========================================");
Console.WriteLine("Error: " + ex.Message);
Console.WriteLine(ex.StackTrace);
Console.WriteLine("=========================================");
Thread.Sleep(2000);
return -10;
}
}
static int Main(string[] args)
{
try
{
// Handles a bug in .NET console applications
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
// Get the version number
var assembly = Assembly.GetExecutingAssembly();
var assemblyVersion = assembly.GetName().Version.ToString();
Console.WriteLine("CrossLinkingIMS Console Application Version " + assemblyVersion);
var commandLineUtil = new CommandLineUtil(caseSensitiveSwitchNames: false);
// Make sure we have parameters. If not, then show the user the proper syntax
var doParametersExist = commandLineUtil.ParseCommandLine();
if (!doParametersExist)
{
ShowSyntax();
return(-1);
}
// Get the Feature File Location
string featureFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("f", out featureFileLocation))
{
Console.WriteLine("-f switch is missing");
ShowSyntax();
return(-2);
}
if (!FileExists(featureFileLocation))
{
return(-4);
}
var featureFile = new FileInfo(featureFileLocation);
// Get the Peaks File Location
string peaksFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("p", out peaksFileLocation))
{
Console.WriteLine("-p switch is missing");
ShowSyntax();
return(-2);
}
if (!FileExists(peaksFileLocation))
{
return(-4);
}
var peaksFile = new FileInfo(peaksFileLocation);
// Get the FastA File Location
string fastAFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("fasta", out fastAFileLocation))
{
Console.WriteLine("-fasta switch is missing");
ShowSyntax();
return(-2);
}
if (!FileExists(fastAFileLocation))
{
return(-4);
}
var fastAFile = new FileInfo(fastAFileLocation);
// Get the PPM Mass Tolerance
string massToleranceString;
if (!commandLineUtil.RetrieveValueForParameter("ppm", out massToleranceString))
{
Console.WriteLine("-ppm switch is missing");
ShowSyntax();
return(-2);
}
var massTolerance = double.Parse(massToleranceString);
// Get the Max Missed Cleavages
string maxMissedCleavagesString;
commandLineUtil.RetrieveValueForParameter("c", out maxMissedCleavagesString);
if (string.IsNullOrEmpty(maxMissedCleavagesString))
{
maxMissedCleavagesString = "1";
}
var maxMissedCleavages = int.Parse(maxMissedCleavagesString);
// Get the Partially Tryptic Flag
string trypticString;
commandLineUtil.RetrieveValueForParameter("t", out trypticString);
string staticDeltaMassString;
var staticDeltaMass = 0.0;
if (commandLineUtil.RetrieveValueForParameter("static", out staticDeltaMassString))
{
double.TryParse(staticDeltaMassString, out staticDeltaMass);
}
var useC13 = true;
var useN15 = true;
if (commandLineUtil.IsParameterPresent("c13off"))
{
useC13 = false;
}
if (commandLineUtil.IsParameterPresent("n15off"))
{
useN15 = false;
}
if (!(useC13 || useN15) && Math.Abs(staticDeltaMass) < float.Epsilon)
{
Console.WriteLine("If you use both -C13off and -N15off, you must use -Static:MassDiff to specify a static mass difference");
Thread.Sleep(1500);
return(-3);
}
var settings = new CrossLinkSettings(massTolerance, maxMissedCleavages, trypticString, useC13, useN15, staticDeltaMass);
// Get the Output File Location
string outputFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("o", out outputFileLocation))
{
if (featureFile.DirectoryName != null && featureFile.DirectoryName == peaksFile.DirectoryName)
{
outputFileLocation = Path.Combine(featureFile.DirectoryName, "crossLinkResults.csv");
}
else
{
outputFileLocation = "crossLinkResults.csv";
}
}
// Run the cross-linking application
Console.WriteLine("Executing...");
var crossLinkResults = CrossLinkingImsController.Execute(settings, fastAFile, featureFile, peaksFile);
var outputFileInfo = new FileInfo(outputFileLocation);
// Output the results
Console.WriteLine("Outputting " + crossLinkResults.Count().ToString("#,##0") + " results to \n" + outputFileInfo.FullName);
CrossLinkUtil.OutputCrossLinkResults(crossLinkResults, outputFileInfo);
return(0);
}
catch (Exception ex)
{
Console.WriteLine();
Console.WriteLine("=========================================");
Console.WriteLine("Error: " + ex.Message);
Console.WriteLine(ex.StackTrace);
Console.WriteLine("=========================================");
Thread.Sleep(2000);
return(-10);
}
}
