/// <summary>
/// This event is fired when OpenFileDialog raises this event
/// indicating that the user has selected to run the QC analysis
/// </summary>
/// <param name="sender">OpenFileDialog</param>
/// <param name="e">OpenFileDialog arguments</param>
private void OnRunStartClicked(object sender, OpenFileArgs e)
{
run = new RunProgressDialog();
run.StartRun += new EventHandler(this.OnRunQcAnalysisStarted);
run.CancelRun += new EventHandler(this.OnCancelAnalysisClicked);
run.Args = e;
run.Owner = this;
this.IsEnabled = false;
run.ShowDialog();
this.IsEnabled = true;
}
/// <summary>
/// This event is fired by analysisThread when the thread is invoked.
/// This event calls the main Qc application framework and executes the analysis.
/// </summary>
/// <param name="sender">BackgroundWorker instance</param>
/// <param name="e">Event parameters</param>
private void DoQcAnalysis(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
if (worker != null)
{
try
{
OpenFileArgs args = e.Argument as OpenFileArgs;
System.Windows.Threading.Dispatcher dispatcher = run.Dispatcher;
UpdateProgressDelegate update = new UpdateProgressDelegate(UpdateProgressText);
if (args != null)
{
dispatcher.BeginInvoke(update, 0, "Starting analysis...please be patient!");
application = new Seqcos(args.InputInfo.Parser, args.InputInfo.Filename, args.CanRunSequenceQc, args.CanRunQualityScoreQc, args.CanRunBlast, args.FastqFormat);
#region Sequence-level QC
/// Run sequence level QC
if (args.CanRunSequenceQc)
{
// Content by position
dispatcher.BeginInvoke(update, 25, "Performing sequence-level QC...analyzing base positions");
application.SequenceQc.ContentByPosition();
dispatcher.BeginInvoke(update, 45, "Performing sequence-level QC...analyzing base positions");
application.SequenceQc.GCContentByPosition();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
// Content by sequence
dispatcher.BeginInvoke(update, 65, "Performing sequence-level QC...analyzing sequences");
application.SequenceQc.ContentBySequence();
dispatcher.BeginInvoke(update, 85, "Performing sequence-level QC...analyzing sequences");
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
// Plot results
dispatcher.BeginInvoke(update, 80, "Generating plots...");
application.PlotSequenceLevelStats();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Send, update, 100, "Done sequence-level QC!");
}
#endregion
#region Quality score-level QC
/// Run quality score level QC
if (args.CanRunQualityScoreQc)
{
dispatcher.BeginInvoke(update, 5, "Performing quality score-level QC...analyzing base positions");
application.QualityScoreQc.ContentByPosition();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.BeginInvoke(update, 25, "Performing quality score-level QC...analyzing sequences");
application.QualityScoreQc.ContentBySequence();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.BeginInvoke(update, 55, "Generating plots (the boxplot will take a while...please be patient!)");
application.PlotQualityScoreLevelStats();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Send, update, 100, "Done quality score-level QC!");
}
application.WriteInputStatistics(excelFormat: false);
application.FinishQualityScoreQC();
#endregion
#region BLAST
/// Run BLAST
if (args.CanRunBlast)
{
dispatcher.BeginInvoke(update, 10, "Generating temporary FASTA file for BLAST...");
// execute BLAST here..
string targetFasta = application.OutputDirectory + "/" + application.GetPrefix() + ".fa";
BioHelper.ConvertToFASTA(application.ContaminationFinder.TargetSequences, targetFasta, args.BlastArgs.NumInputSequences, false);
dispatcher.BeginInvoke(update, 70, "Running BLAST...");
application.ContaminationFinder.RunLocalBlast(args.BlastArgs.Database, targetFasta);
dispatcher.BeginInvoke(update, 100, "Finished! Deleting FASTA file...");
File.Delete(targetFasta);
}
#endregion
}
}
catch (ArgumentNullException ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
catch (Exception ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
}
}
