private bool ExistDa(ObservableCollection <ProteinDbForDataGrid> pDOC, ProteinDbForDataGrid uuu)
{
foreach (ProteinDbForDataGrid pdoc in pDOC)
{
if (pdoc.FilePath == uuu.FilePath)
{
return(true);
}
}
return(false);
}
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;
}
}
