/// <summary>
/// Checks that the ID file that the user has added is valid input. This is called
/// each time a new ID file is added. The method first checks that the ID header is
/// interpretable and then attempts to read the first identification. A popup is displayed
/// if there is an error.
/// </summary>
private bool ValidateIdentificationFile(IdentificationFileForDataGrid idFile)
{
//TODO
bool valid = true;
return(valid);
}
/// <summary>
/// Deletes a file (ID or spectra file) from the data grid.
/// </summary>
private void DeleteFileFromGrid_Click(object sender, RoutedEventArgs e)
{
SpectraFileForDataGrid spectraFile = (sender as Button).DataContext as SpectraFileForDataGrid;
if (spectraFile != null)
{
spectraFiles.Remove(spectraFile);
if (!spectraFiles.Any())
{
DragAndDropHelperLabelSpectraFiles.Visibility = Visibility.Visible;
}
return;
}
IdentificationFileForDataGrid idFile = (sender as Button).DataContext as IdentificationFileForDataGrid;
if (idFile != null)
{
idFiles.Remove(idFile);
if (!idFiles.Any())
{
DragAndDropHelperLabelIdFiles.Visibility = Visibility.Visible;
}
return;
}
}
private void AddAFile(string filePath)
{
string filename = Path.GetFileName(filePath);
string theExtension = Path.GetExtension(filename).ToLowerInvariant();
switch (theExtension)
{
case ".raw":
if (!ThermoStaticData.CheckForMsFileReader())
{
AddNotification("Warning! Cannot find Thermo MSFileReader (v3.0 SP2 is preferred); a crash may result from searching this .raw file");
}
goto case ".mzml";
case ".mzml":
SpectraFileForDataGrid spectraFile = new SpectraFileForDataGrid(filePath);
if (!spectraFilesForDataGrid.Select(f => f.FilePath).Contains(spectraFile.FilePath))
{
spectraFilesForDataGrid.Add(spectraFile);
}
if (string.IsNullOrEmpty(OutputFolderTextBox.Text))
{
var pathOfFirstSpectraFile = Path.GetDirectoryName(spectraFilesForDataGrid.First().FilePath);
OutputFolderTextBox.Text = Path.Combine(pathOfFirstSpectraFile, @"FlashLFQ_$DATETIME");
}
break;
case ".txt":
case ".tsv":
case ".psmtsv":
case ".tabular":
IdentificationFileForDataGrid identFile = new IdentificationFileForDataGrid(filePath);
if (!identFilesForDataGrid.Select(f => f.FilePath).Contains(identFile.FilePath) && !identFile.FileName.Equals("ExperimentalDesign.tsv"))
{
identFilesForDataGrid.Add(identFile);
}
break;
default:
AddNotification("Unrecognized file type: " + theExtension);
break;
}
}
/// <summary>
/// Handles adding a file (spectra or ID file). The source can be by drag+drop or through
/// clicking one of the "Add" buttons.
/// </summary>
private void AddAFile(string filePath)
{
string filename = Path.GetFileName(filePath);
string theExtension = Path.GetExtension(filename).ToLowerInvariant();
if (theExtension == ".raw")
{
var licenceAgreement = LicenceAgreementSettings.ReadLicenceSettings();
if (!licenceAgreement.HasAcceptedThermoLicence)
{
var thermoLicenceWindow = new ThermoLicenceAgreementWindow();
thermoLicenceWindow.LicenceText.AppendText(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
var dialogResult = thermoLicenceWindow.ShowDialog();
if (dialogResult.HasValue && dialogResult.Value == true)
{
try
{
licenceAgreement.AcceptLicenceAndWrite();
}
catch (Exception e)
{
MessageBox.Show(e.Message);
}
}
else
{
return;
}
}
}
switch (theExtension)
{
case ".raw":
case ".mzml":
List <int> existingDefaultSampleNumbers = spectraFiles.Where(p => p.Condition == DefaultCondition)
.Select(p => p.Sample)
.Distinct()
.OrderBy(p => p).ToList();
int sampleNumber = 1;
for (int i = 1; i < int.MaxValue; i++)
{
if (!existingDefaultSampleNumbers.Contains(i))
{
sampleNumber = i;
break;
}
}
SpectraFileForDataGrid spectraFile = new SpectraFileForDataGrid(filePath, DefaultCondition, sampleNumber, 1, 1);
if (!spectraFiles.Select(f => f.FilePath).Contains(spectraFile.FilePath))
{
CheckForExistingExperimentalDesignFile(spectraFile);
spectraFiles.Add(spectraFile);
DragAndDropHelperLabelSpectraFiles.Visibility = Visibility.Hidden;
}
if (string.IsNullOrEmpty(OutputFolderTextBox.Text))
{
var pathOfFirstSpectraFile = Path.GetDirectoryName(spectraFiles.First().FilePath);
OutputFolderTextBox.Text = Path.Combine(pathOfFirstSpectraFile, @"FlashLFQ_$DATETIME");
}
break;
case ".txt":
case ".tsv":
case ".psmtsv":
case ".tabular":
IdentificationFileForDataGrid identFile = new IdentificationFileForDataGrid(filePath);
if (!idFiles.Select(f => f.FilePath).Contains(identFile.FilePath) && !identFile.FileName.Equals("ExperimentalDesign.tsv"))
{
bool valid = ValidateIdentificationFile(identFile);
if (valid)
{
idFiles.Add(identFile);
DragAndDropHelperLabelIdFiles.Visibility = Visibility.Hidden;
}
}
break;
default:
//TODO: change this to popup
AddNotification("Unrecognized file type: " + theExtension);
break;
}
}
