public void ValidateCommandLineSettings()
{
Spectra = _spectra == null ? new List <string>() : _spectra.ToList();
Tasks = _tasks == null ? new List <string>() : _tasks.ToList();
Databases = _databases == null ? new List <string>() : _databases.ToList();
if ((GenerateDefaultTomls || RunMicroVignette) && OutputFolder == null)
{
throw new MetaMorpheusException("An output path must be specified with the -o parameter.");
}
if (GenerateDefaultTomls || RunMicroVignette)
{
return;
}
if (OutputFolder == null && Spectra.Count < 1 && Tasks.Count < 1 && Databases.Count < 1 && Spectra.Count < 1)
{
throw new MetaMorpheusException("Use the --help parameter to view all parameters (e.g., \"CMD.exe --help\")");
}
if (OutputFolder == null && Spectra.Count > 0)
{
var pathOfFirstSpectraFile = Path.GetDirectoryName(Spectra.First());
OutputFolder = Path.Combine(pathOfFirstSpectraFile, @"$DATETIME");
}
if (Tasks.Count < 1)
{
throw new MetaMorpheusException("At least one task must be specified.");
}
if (Databases.Count < 1)
{
throw new MetaMorpheusException("At least one protein database must be specified.");
}
if (Spectra.Count < 1)
{
throw new MetaMorpheusException("At least one spectra file must be specified.");
}
// add spectra files from specified directories
List <string> spectraFromDirectories = new List <string>();
foreach (string item in Spectra)
{
if (Directory.Exists(item))
{
string[] directoryFiles = Directory.GetFiles(item);
foreach (var file in directoryFiles)
{
if (GlobalVariables.AcceptedSpectraFormats.Contains(GlobalVariables.GetFileExtension(file).ToLowerInvariant()))
{
spectraFromDirectories.Add(file);
if (Verbosity == VerbosityType.normal)
{
Console.WriteLine("Found spectra file: " + file);
}
}
}
}
else if (!File.Exists(item))
{
throw new MetaMorpheusException("The following is not a known file or directory: " + item);
}
}
Spectra.AddRange(spectraFromDirectories);
// remove spectra directories, after their spectra files have been added
Spectra.RemoveAll(p => Directory.Exists(p));
IEnumerable <string> fileNames = Tasks.Concat(Databases).Concat(Spectra);
foreach (string filename in fileNames)
{
if (!File.Exists(filename))
{
throw new MetaMorpheusException("The following file does not exist: " + filename);
}
}
foreach (string filename in Tasks)
{
string ext = Path.GetExtension(filename).ToLowerInvariant();
if (ext != ".toml")
{
throw new MetaMorpheusException("Tasks must be in .toml file format. Unrecognized file format: " + ext);
}
}
foreach (string filename in Databases)
{
string ext = Path.GetExtension(filename).ToLowerInvariant();
bool compressed = ext.EndsWith("gz"); // allows for .bgz and .tgz, too which are used on occasion
ext = compressed ? Path.GetExtension(Path.GetFileNameWithoutExtension(filename)).ToLowerInvariant() : ext;
if (!GlobalVariables.AcceptedDatabaseFormats.Contains(ext))
{
throw new MetaMorpheusException("Unrecognized protein database file format: " + ext);
}
}
foreach (string filename in Spectra)
{
string ext = Path.GetExtension(filename).ToLowerInvariant();
if (!GlobalVariables.AcceptedSpectraFormats.Contains(ext))
{
throw new MetaMorpheusException("Unrecognized spectra file format: " + ext);
}
}
}
