private void AddNeoTaskButton_Click(object sender, RoutedEventArgs e)
{
var dialog = new NeoSearchTaskWindow();
if (dialog.ShowDialog() == true)
{
var ye5 = dialog.TheTask;
foreach (MetaMorpheusTask task in NeoLoadTomls.LoadTomls(ye5))
{
AddTaskToCollection(task);
}
UpdateTaskGuiStuff();
}
}
private static void Main(string[] args)
{
Console.WriteLine("Welcome to MetaMorpheus");
Console.WriteLine(GlobalVariables.MetaMorpheusVersion);
var p = new FluentCommandLineParser <ApplicationArguments>();
p.Setup(arg => arg.Tasks)
.As('t', "tasks")
.SetDefault(new List <string>());
p.Setup(arg => arg.MetaTasks)
.As('m', "meta-task")
.SetDefault(new List <string>());
p.Setup(arg => arg.Spectra)
.As('s', "spectra")
.Required();
p.Setup(arg => arg.Databases)
.As('d', "databases")
.Required();
var result = p.Parse(args);
if (p.Object.MetaTasks.Count != 0 || p.Object.Tasks.Count != 0)
{
if (!result.HasErrors)
{
MetaMorpheusEngine.WarnHandler += WarnHandler;
MetaMorpheusEngine.OutProgressHandler += MyEngine_outProgressHandler;
MetaMorpheusEngine.StartingSingleEngineHander += MyEngine_startingSingleEngineHander;
MetaMorpheusEngine.FinishedSingleEngineHandler += MyEngine_finishedSingleEngineHandler;
MetaMorpheusTask.WarnHandler += WarnHandler;
MetaMorpheusTask.LogHandler += LogHandler;
MetaMorpheusTask.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
foreach (var db in p.Object.Databases)
{
if (!Path.GetExtension(db).Equals(".fasta"))
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(db).OfType <ModificationWithLocation>());
}
}
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>();
for (int i = 0; i < p.Object.Tasks.Count; i++)
{
var filePath = p.Object.Tasks[i];
var uhum = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (uhum.Get <string>("TaskType"))
{
case "Search":
var ye1 = Toml.ReadFile <SearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "SearchTask", ye1));
break;
case "Calibrate":
var ye2 = Toml.ReadFile <CalibrationTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "CalibrationTask", ye2));
break;
case "Gptmd":
var ye3 = Toml.ReadFile <GptmdTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GptmdTask", ye3));
break;
case "XLSearch":
var ye4 = Toml.ReadFile <XLSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "XLSearchTask", ye4));
break;
case "Neo":
Console.WriteLine("Neo tasks are meta-tasks that rely on several other tasks. Please use -m for meta instead of -t. Skipping.");
break;
default:
Console.WriteLine(uhum.Get <string>("TaskType") + " is not a known task type! Skipping.");
break;
}
}
for (int i = 0; i < p.Object.MetaTasks.Count; i++)
{
var filePath = p.Object.MetaTasks[i];
var uhum = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (uhum.Get <string>("TaskType"))
{
case "Search":
Console.WriteLine("Search tasks are individual tasks. Please use -t for task instead of -m. Skipping.");
break;
case "Calibrate":
Console.WriteLine("Calibrate tasks are individual tasks. Please use -t for task instead of -m. Skipping.");
break;
case "Gptmd":
Console.WriteLine("Gptmd tasks are individual tasks. Please use -t for task instead of -m. Skipping.");
break;
case "XLSearch":
Console.WriteLine("XLSearch tasks are individual tasks. Please use -t for task instead of -m. Skipping.");
break;
case "Neo":
var ye5 = Toml.ReadFile <NeoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
foreach (MetaMorpheusTask task in NeoLoadTomls.LoadTomls(ye5))
{
taskList.Add(("Task" + (taskList.Count + 1) + ye5.TaskType, ye5));
}
break;
default:
Console.WriteLine(uhum.Get <string>("TaskType") + " is not a known task type! Skipping.");
break;
}
}
List <string> startingRawFilenameList = p.Object.Spectra.Select(b => Path.GetFullPath(b)).ToList();
List <DbForTask> startingXmlDbFilenameList = p.Object.Databases.Select(b => new DbForTask(Path.GetFullPath(b), IsContaminant(b))).ToList();
var MatchingChars =
from len in Enumerable.Range(0, startingRawFilenameList.Min(s => s.Length)).Reverse()
let possibleMatch = startingRawFilenameList.First().Substring(0, len)
where startingRawFilenameList.All(f => f.StartsWith(possibleMatch, StringComparison.Ordinal))
select possibleMatch;
string outputFolder = Path.Combine(Path.GetDirectoryName(MatchingChars.First()), @"$DATETIME");
EverythingRunnerEngine a = new EverythingRunnerEngine(taskList, startingRawFilenameList, startingXmlDbFilenameList, outputFolder);
try
{
a.Run();
}
catch (Exception e)
{
while (e.InnerException != null)
{
e = e.InnerException;
}
var message = "Run failed, Exception: " + e.Message;
Console.WriteLine(message);
}
}
else
{
Console.WriteLine("Error Text:" + result.ErrorText);
}
}
else
{
Console.WriteLine("Error Text: No toml file was specified. Use -t for tasks or -m for meta-tasks.");
}
}
private void AddAFile(string draggedFilePath)
{
// this line is NOT used because .xml.gz (extensions with two dots) mess up with Path.GetExtension
//var theExtension = Path.GetExtension(draggedFilePath).ToLowerInvariant();
// we need to get the filename before parsing out the extension because if we assume that everything after the dot
// is the extension and there are dots in the file path (i.e. in a folder name), this will mess up
var filename = Path.GetFileName(draggedFilePath);
var theExtension = filename.Substring(filename.IndexOf(".")).ToLowerInvariant();
switch (theExtension)
{
case ".raw":
var versionCheckerResult = MyFileManager.ValidateThermoMsFileReaderVersion();
if (versionCheckerResult.Equals(MyFileManager.ThermoMsFileReaderVersionCheck.IncorrectVersion))
{
GuiWarnHandler(null, new StringEventArgs("Warning! Thermo MSFileReader is not version 3.0 SP2; a crash may result from searching this .raw file", null));
}
else if (versionCheckerResult.Equals(MyFileManager.ThermoMsFileReaderVersionCheck.DllsNotFound))
{
GuiWarnHandler(null, new StringEventArgs("Warning! Cannot find Thermo MSFileReader (v3.0 SP2 is preferred); a crash may result from searching this .raw file", null));
}
goto case ".mzml";
case ".mzml":
RawDataForDataGrid zz = new RawDataForDataGrid(draggedFilePath);
if (!ExistRaw(rawDataObservableCollection, zz))
{
rawDataObservableCollection.Add(zz);
}
UpdateFileSpecificParamsDisplayJustAdded(Path.ChangeExtension(draggedFilePath, ".toml"));
UpdateOutputFolderTextbox();
break;
case ".mzml.gz": // not implemented yet
case ".fasta.gz": // not implemented yet
GuiWarnHandler(null, new StringEventArgs("Cannot read, try uncompressing: " + draggedFilePath, null));
break;
case ".xml":
case ".xml.gz":
case ".fasta":
case ".fa":
ProteinDbForDataGrid uu = new ProteinDbForDataGrid(draggedFilePath);
if (!ExistDa(proteinDbObservableCollection, uu))
{
proteinDbObservableCollection.Add(uu);
if (theExtension.Equals(".xml") || theExtension.Equals(".xml.gz"))
{
try
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(draggedFilePath).OfType <ModificationWithLocation>());
}
catch (Exception ee)
{
MessageBox.Show(ee.ToString());
GuiWarnHandler(null, new StringEventArgs("Cannot read: " + draggedFilePath, null));
proteinDbObservableCollection.Remove(uu);
}
}
}
break;
case ".toml":
var tomlFile = Toml.ReadFile(draggedFilePath, MetaMorpheusTask.tomlConfig);
if (tomlFile.Keys.Contains("PrecursorMassTolerance") && tomlFile.Keys.Contains("ProductMassTolerance") && tomlFile.Keys.Count == 2)
{
// do nothing; it's a ppm suggested tolerance toml from calibration, this gets read in elsewhere
}
else
{
try
{
switch (tomlFile.Get <string>("TaskType"))
{
case "Search":
var ye1 = Toml.ReadFile <SearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye1);
break;
case "Calibrate":
var ye2 = Toml.ReadFile <CalibrationTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye2);
break;
case "Gptmd":
var ye3 = Toml.ReadFile <GptmdTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye3);
break;
case "XLSearch":
var ye4 = Toml.ReadFile <XLSearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye4);
break;
case "Neo":
var ye5 = Toml.ReadFile <NeoSearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
foreach (MetaMorpheusTask task in NeoLoadTomls.LoadTomls(ye5))
{
AddTaskToCollection(task);
}
break;
}
}
catch (Exception e)
{
GuiWarnHandler(null, new StringEventArgs("Could not parse .toml: " + e.Message, null));
}
}
break;
default:
GuiWarnHandler(null, new StringEventArgs("Unrecognized file type: " + theExtension, null));
break;
}
}
