private void embedAllButton_Click(object sender, EventArgs e)
{
var searchPath = new StringBuilder(searchPathTextBox.Text);
string extensions = extensionsTextBox.Text;
Application.UseWaitCursor = true;
deleteAllButton.Enabled = embedAllButton.Enabled = false;
embeddedChanges = true;
try
{
// add location of original idpDBs to the search path
var mergedFilepaths = session.CreateSQLQuery("SELECT DISTINCT Filepath FROM MergedFiles").List <string>();
foreach (var filepath in mergedFilepaths)
{
searchPath.AppendFormat(";{0}", System.IO.Path.GetDirectoryName(filepath));
}
}
catch
{
// ignore if MergedFiles does not exist
}
var quantitationMethodBySource = new Dictionary <int, Embedder.QuantitationConfiguration>();
var xicConfigBySource = new Dictionary <int, Embedder.XICConfiguration> {
{ 0, _defaultXicConfig }
};
foreach (DataGridViewRow row in dataGridView.Rows)
{
int id = (int)row.Cells[idColumn.Index].Value;
var method = QuantitationMethodForRow(row.Index);
if (IsLabelFree(method))
{
xicConfigBySource[id] = (Embedder.XICConfiguration)row.Cells[quantitationSettingsColumn.Index].Value;
quantitationMethodBySource[id] = new Embedder.QuantitationConfiguration(QuantitationMethod.LabelFree, _defaultIsobaricConfig.ToString());
}
else if (IsIsobaric(method))
{
quantitationMethodBySource[id] = (Embedder.QuantitationConfiguration)row.Cells[quantitationSettingsColumn.Index].Value;
}
}
okButton.Text = "Cancel";
EmbedInProgress = true;
new Thread(() =>
{
try
{
var ilr = new IterationListenerRegistry();
ilr.addListener(new EmbedderIterationListener(this), 1);
var tempFolder = string.Empty;
var splitSourceList = new List <List <string> >();
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)) && xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
tempFolder = getTempFolder();
splitSourceList = GetRTAlignGroups();
}
string idpDbFilepath = session.Connection.GetDataSource();
if (embedScanTimeOnlyBox.Checked)
{
Embedder.EmbedScanTime(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
}
else
{
Embedder.Embed(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, ilr);
}
if (quantitationMethodBySource.Any(x => IsLabelFree(x.Value.QuantitationMethod)))
{
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = false));
if (xicConfigBySource.Any(x => x.Value.AlignRetentionTime))
{
try
{
RTAlignPreparations(splitSourceList, tempFolder);
foreach (var kvp in xicConfigBySource)
{
kvp.Value.RTFolder = tempFolder;
}
}
catch (Exception rtError)
{
MessageBox.Show("Error: Cannot prepare RT alignment. Skipping to next stage." +
Environment.NewLine + rtError.Message);
foreach (var kvp in xicConfigBySource)
{
kvp.Value.AlignRetentionTime = false;
}
}
}
Embedder.EmbedMS1Metrics(idpDbFilepath, searchPath.ToString(), extensions, quantitationMethodBySource, xicConfigBySource, ilr);
if (!string.IsNullOrEmpty(tempFolder) && Directory.Exists(tempFolder))
{
Directory.Delete(tempFolder, true);
}
BeginInvoke(new MethodInvoker(() => ModeandDefaultPanel.Visible = true));
}
}
catch (Exception ex)
{
if (ex.Message.Contains("QuantitationConfiguration"))
{
string message = ex.Message.Replace("[QuantitationConfiguration] ", "");
message = Char.ToUpper(message[0]) + message.Substring(1);
MessageBox.Show(message);
}
else if (ex.Message.Contains("no filepath"))
{
bool multipleMissingFilepaths = ex.Message.Contains("\n");
string missingFilepaths = ex.Message.Replace("\n", "\r\n");
missingFilepaths = missingFilepaths.Replace("[embed] no", "No");
missingFilepaths = missingFilepaths.Replace("[embedScanTime] no", "No");
MessageBox.Show(missingFilepaths + "\r\n\r\nCheck that " +
(multipleMissingFilepaths ? "these source files" : "this source file") +
" can be found in the search path with one of the specified extensions.");
}
else
{
Program.HandleException(ex);
}
}
BeginInvoke(new MethodInvoker(() => Refresh()));
}).Start();
}
