public void TestGeneratingMs1FeatureFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_2\QC_ShewIntact_1_19Jun15_Bane_14-09-01RZ.pbf";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const string outFolderPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\Output";
if (!Directory.Exists(outFolderPath))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, outFolderPath);
}
//const string specFilePath = @"D:\MassSpecFiles\test\QC_Shew_Intact_4_01Jan15_Bane_C2-14-08-02RZ.raw";
const int minScanCharge = 2;
const int maxScanCharge = 60;
const double minScanMass = 3000;
const double maxScanMass = 5000;
const int maxThreads = 10;
var param = new LcMsFeatureFinderInputParameter()
{
InputPath = specFilePath,
OutputPath = outFolderPath,
MinSearchMass = minScanMass,
MaxSearchMass = maxScanMass,
MinSearchCharge = minScanCharge,
MaxSearchCharge = maxScanCharge,
CsvOutput = true,
ScoreReport = false,
MaxThreads = maxThreads
};
var featureFinder = new LcMsFeatureFinderLauncher(param);
featureFinder.Run();
}
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
}
static int Main(string[] args)
{
try
{
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"};
if (args.Length == 0)
{
PrintUsageInfo();
return(-1);
}
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return(-1);
}
// initialize parameters
_paramDic = new Dictionary <string, string>
{
{ LcMsFeatureFinderInputParameter.INPUT_FILE_PATH, null },
{ LcMsFeatureFinderInputParameter.OUTPUT_FOLDER_PATH, null },
{ LcMsFeatureFinderInputParameter.MINIMUM_CHARGE, "1" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_CHARGE, "60" },
{ LcMsFeatureFinderInputParameter.MINIMUM_MASS, "2000.0" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_MASS, "50000.0" },
{ LcMsFeatureFinderInputParameter.INCLUDE_ADDITIONAL_SCORES, "n" },
{ LcMsFeatureFinderInputParameter.SAVE_CSV, "n" },
{ LcMsFeatureFinderInputParameter.SAVE_PNG_FEATURE_MAP, "y" },
{ LcMsFeatureFinderInputParameter.LIKELIHOOD_SCORE_THRESHOLD, "-10" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_THREADS, "0" },
{ LcMsFeatureFinderInputParameter.EXISTING_MS1FT_FILE, "" }
};
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
var inputFilePath = _paramDic["-i"];
if (inputFilePath == null)
{
PrintUsageInfo("Missing required parameter -i!");
return(-1);
}
if (!File.Exists(inputFilePath) && !Directory.Exists(inputFilePath))
{
PrintUsageInfo("File not found: " + inputFilePath);
return(-1);
}
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
{
#endif
var param = new LcMsFeatureFinderInputParameter(_paramDic);
Console.WriteLine("************ {0} {1} ************", Name, Version);
param.Display();
var launcher = new LcMsFeatureFinderLauncher(param);
int errorCode;
if (string.IsNullOrWhiteSpace(param.ExistingFeaturesFilePath))
{
errorCode = launcher.Run();
}
else
{
errorCode = launcher.CreateFeatureMapImage(param.InputPath, param.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
}