private void Form1_FormClosing(object sender, FormClosingEventArgs e)
{
if (MainThread != null && MainThread.IsAlive)
{
MainThread.Abort();
}
if (Hoarder != null)
{
//Hoarder.UpdateLog -= new EventHandler<StatusEventArgs>(hoarder_UpdateLog);
//Hoarder.UpdateProgress -= new EventHandler<ProgressEventArgs>(hoarder_UpdateProgress);
Hoarder = null;
}
Properties.Settings.Default.Save();
e.Cancel = false;
}
public void UpdateProgress(double percent)
{
if (InvokeRequired)
{
if (Hoarder != null)
{
Invoke(new UpdateProgressDelegate(UpdateProgress), new object[] { percent });
}
}
else
{
// If the precent is less than zero, the program is finished
if (percent < 0)
{
hoardB.Enabled = true;
outputGB.Enabled = true;
inputGB.Enabled = true;
optionsGB.Enabled = true;
quantGB.Enabled = true;
progressBar.Style = ProgressBarStyle.Continuous;
progressBar.Value = 0;
WriteLog();
Hoarder.UpdateLog -= hoarder_UpdateLog;
Hoarder.UpdateProgress -= hoarder_UpdateProgress;
Hoarder = null;
}
else if (percent == 0.0)
{
progressBar.Style = ProgressBarStyle.Marquee;
progressBar.Value = 0;
}
else
{
progressBar.Style = ProgressBarStyle.Blocks;
progressBar.Value = (int)(10000 * percent);
}
}
}
public void Run()
{
string fastaFile = databaseTB.Text;
if (!System.IO.File.Exists(fastaFile))
{
UpdateLog("Cannot find protein database " + fastaFile + ", aborting!");
return;
}
string outputDirectory = outputTB.Text;
if (string.IsNullOrWhiteSpace(outputDirectory))
{
UpdateLog("Must provide a valid output folder!");
return;
}
if (!System.IO.Directory.Exists(outputDirectory))
{
UpdateLog("Output directory " + outputDirectory + " doesn't exist, creating it...");
System.IO.Directory.CreateDirectory(outputDirectory);
}
int minPeptidesperGroup = (int)minpepspergroupUD.Value;
int maxMissedCleavage = (int)maxMissedCleavagedUD.Value;
double maxFDR = (double)fdrUD.Value;
bool useConservative = conservativeCB.Checked;
bool useQuant = enableQuantCB.Checked;
//bool filterinterference = quantigorneinterferenceCB.Checked;
bool includeUnfiltereedResults = includeUnfliterCB.Checked;
bool ignorePeptidesWithMissingData = ignorePepMissingCB.Checked;
bool semiDigestion = semiCB.Checked;
bool proteinPerMin = proteinsPerMinCB.Checked;
bool duplexQuant = duplexCB.Enabled && duplexCB.Checked;
bool useMedian = medianvalueCB.Enabled && medianvalueCB.Checked;
bool useNoiseBandCap = useNBCCB.Enabled && useNBCCB.Checked;
bool sequenceCoverageMap = sequenceMapCB.Enabled && sequenceMapCB.Checked;
AnnotationType annotationType = (AnnotationType)comboBox1.SelectedItem;
//double interferencecutoff = (double)quantintferenceUD.Value;
HashSet <Modification> modstoignore = new HashSet <Modification>();
if (useQuant)
{
foreach (string modName in ignoreModsCLB.CheckedItems.Cast <string>())
{
Modification mod = new Modification(modName, true);
// mod.IgnoreMod = true;
modstoignore.Add(mod);
}
}
logTB.Clear();
Hoarder = new ProteinHoarder(CsvFiles, fastaFile, outputDirectory, minPeptidesperGroup, maxMissedCleavage, maxFDR, annotationType, useConservative, useQuant, useMedian, duplexQuant, useNoiseBandCap, modstoignore, false, 0.0, includeUnfiltereedResults, ignorePeptidesWithMissingData, semiDigestion, proteinPerMin, sequenceCoverageMap);
Hoarder.UpdateLog += new EventHandler <StatusEventArgs>(hoarder_UpdateLog);
Hoarder.UpdateProgress += new EventHandler <ProgressEventArgs>(hoarder_UpdateProgress);
MainThread = new Thread(Hoarder.Herd);
MainThread.IsBackground = true;
MainThread.Start();
hoardB.Enabled = false;
outputGB.Enabled = false;
inputGB.Enabled = false;
optionsGB.Enabled = false;
quantGB.Enabled = false;
}
