private void PopulateChoices()
{
//CmbxExperimentType.Items.Add(ExperimentType.RNASequencing.ToString());
//CmbxExperimentType.Items.Add(ExperimentType.WholeGenomeSequencing.ToString());
//CmbxExperimentType.Items.Add(ExperimentType.ExomeSequencing.ToString());
//CmbxExperimentType.SelectedIndex = 0; // hard coded selection (for now)
EnsemblReleases = EnsemblRelease.GetReleases();
}
protected void SaveButton_Click(object sender, RoutedEventArgs e)
{
//// Experiment type selection
//int iii = CmbxExperimentType.SelectedIndex;
//if (iii == 0)
//{
// Options.ExperimentType = ExperimentType.RNASequencing.ToString();
//}
//else if (iii == 1)
//{
// Options.ExperimentType = ExperimentType.WholeGenomeSequencing.ToString();
//}
//else if (iii == 2)
//{
// Options.ExperimentType = ExperimentType.ExomeSequencing.ToString();
//}
//else
//{
// MessageBox.Show("Please choose an experiment type selection.");
// return;
//}
Options.AnalysisDirectory = TrimQuotesOrNull(txtAnalysisDirectory.Text);
try
{
string testDirectory = Path.Combine(Options.AnalysisDirectory, $"TestSpritzPermissions{Options.AnalysisDirectory.GetHashCode()}");
Directory.CreateDirectory(testDirectory);
Directory.Delete(testDirectory);
}
catch (Exception)
{
MessageBox.Show($"Error: Cannot write to specified analysis directory: {Options.AnalysisDirectory}. Please choose another directory.",
"Write Permissions", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}
if (!Directory.Exists(Options.AnalysisDirectory))
{
Directory.CreateDirectory(Options.AnalysisDirectory);
}
Options.Threads = Threads;
EnsemblRelease ensembl = (EnsemblRelease)EnsemblReleaseVersions.SelectedItem;
Options.Release = ensembl.Release;
Options.Species = EnsemblSpecies.SelectedItem.ToString();
Options.Reference = ensembl.Genomes[Options.Species];
Options.Organism = ensembl.Organisms[Options.Species];
Options.AnalyzeVariants = (bool)Cb_AnalyzeVariants.IsChecked;
Options.AnalyzeIsoforms = (bool)Cb_AnalyzeIsoforms.IsChecked;
Options.SpritzVersion = MainWindow.CurrentVersion;
DialogResult = true;
}