private void settingsToolStripMenuItem_Click(object sender, EventArgs e)
{
using (settings setDialog = new settings())
{
setDialog.ShowDialog();
}
}
private void viewerToolStripMenuItem_Click(object sender, EventArgs e)
{
if(File.Exists(Properties.Settings.Default.bamstats_gui))
{
cmdProcess = new Process();
cmdProcess.StartInfo.FileName = "cmd.exe";
cmdProcess.StartInfo.Arguments = @"/C java -Xmx8g -jar " + @" """ + Properties.Settings.Default.bamstats_gui + @"""";
cmdProcess.StartInfo.UseShellExecute = true;
cmdProcess.StartInfo.CreateNoWindow = false;
cmdProcess.StartInfo.RedirectStandardOutput = false;
cmdProcess.Start();
}
else
{
MessageBox.Show("The GUI Jar file does not exist: /r/n/n"+Properties.Settings.Default.bamstats_gui,"BAMster - File Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
using (settings setDialog = new settings())
{
setDialog.ShowDialog();
}
}
}
private void executeBtn_Click(object sender, EventArgs e)
{
if (sampleList.Items.Count > 0)
{
if (executeBtn.Text.ToLower() == "analyze")
{
if (File.Exists(featureBox.Text))
{
//analyze samples
doesnotexist = new StringBuilder();
args = new StringBuilder();
samps = new StringBuilder();
int i = 1;
foreach (string path in sampleList.Items)
{
string bamstatout = Path.GetDirectoryName(path) + @"\bamstats\";
string bamstatFN = bamstatout + Path.GetFileName(path) + "_bamster.csv";
if (!File.Exists(bamstatFN))
{
if (!Directory.Exists(bamstatout))
{
Directory.CreateDirectory(bamstatout);
}
if (File.Exists(path))
{
string fn = Path.GetFileNameWithoutExtension(path);
args.Append("java -Xmx8g -jar " + @"""" + Properties.Settings.Default.bamstats_api + @"""" + " -v simple -f " + @"""" + featureBox.Text + @"""" + " -i " + @"""" + path + @"""" + " -o " + @"""" + bamstatFN + @"""" + " & ");
samps.AppendLine(i + ".) " + fn);
i++;
}
else
{
doesnotexist.Append("-" + path + Environment.NewLine);
}
}
}
if (doesnotexist.Length <= 0)
{
if (File.Exists(Properties.Settings.Default.bamstats_api))
{
DialogResult dialogResult = MessageBox.Show("Ready to start analysis?" + Environment.NewLine + Environment.NewLine + "Samples:" + Environment.NewLine + samps.ToString(), "BAMster - Checkpoint", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (dialogResult == DialogResult.Yes)
{
tabControl.SelectedTab = consoleTab;
terminal.ClearOutput();
resultList.Items.Clear();
utilityBtn.Enabled = false;
executeBtn.Text = "CANCEL";
bamStatus.Text = "Analyzing...";
terminal.StartProcess("cmd.exe", @"/C " + args.ToString(0, args.Length - 2));
}
else { dialogResult = DialogResult.Cancel; }
}
else
{
MessageBox.Show("The API Jar file does not exist: " + Environment.NewLine + Environment.NewLine + Properties.Settings.Default.bamstats_api, "BAMster - File Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
using (settings setDialog = new settings())
{
setDialog.ShowDialog();
}
}
}
else
{
MessageBox.Show("Input contains file(s) that do not exist, see below:" + Environment.NewLine + doesnotexist.ToString(0, doesnotexist.Length - 1), "BAMster - 404 Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Please select a valid bed file.", "BAMster - 404 Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else if (executeBtn.Text.ToLower() == "cancel")
{
bamStatus.Text = "Cancelled!";
terminal.StopProcess();
//cancel analysis
executeBtn.Text = "ANALYZE";
}
}
}
