public ProgressForm(IEnumerable <string> taskNames, IterationListenerRegistry ilr)
{
InitializeComponent();
_progressCellByTaskName = new Dictionary <string, DataGridViewProgressCell>();
_textBoxLogByTaskName = new Dictionary <string, TextBox>();
_lastMessageByTaskName = new Dictionary <string, string>();
_rowByTaskName = new Dictionary <string, DataGridViewRow>();
_tasksDone = 0;
_ilr = ilr;
_ilProxy = new IterationListenerProxy()
{
form = this
};
_ilr.addListener(_ilProxy, 1000);
var boxShown = false;
foreach (var task in taskNames)
{
var textBox = _textBoxLogByTaskName[task] = new TextBox
{
Text = String.Format("{0}{1}{0}Starting...{0}",
Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
{
textBox.Visible = false;
}
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
JobDataView.Rows.Add(task, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = textBox;
_rowByTaskName[task] = row;
_progressCellByTaskName[task] = row.Cells[1] as DataGridViewProgressCell;
_progressCellByTaskName[task].Text = "waiting";
}
}
void processFile(string filename, Config config, ReaderList readers)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...", filename);
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
}
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
{
throw new ArgumentException("Output filepath is the same as input filepath");
}
if (StatusUpdate != null)
{
StatusUpdate("Waiting...", ProgressBarStyle.Marquee, _info);
}
// only one thread
lock (calculateSHA1Mutex)
{
if (LogUpdate != null)
{
LogUpdate("Calculating SHA1 checksum...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
}
MSDataFile.calculateSHA1Checksums(msd);
}
if (LogUpdate != null)
{
LogUpdate("Processing...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
}
SpectrumListFactory.wrap(msd, config.Filters);
if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty())
{
if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty())
{
msg = "Note: input contains only chromatogram data.";
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_MZ5:
case MSDataFile.Format.Format_mzML:
break;
default:
msg += " The selected output format can only represent spectra. Consider using mzML instead.";
break;
}
}
else
{
msg = "Note: input contains no spectra or chromatogram data.";
}
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Continuous, _info);
}
}
if (StatusUpdate != null && msd.run.spectrumList != null)
{
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
}
// write out the new data file
var ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
msg = String.Format("Writing \"{0}\"...", outputFilename);
if (LogUpdate != null)
{
LogUpdate(msg, _info);
}
if (StatusUpdate != null)
{
StatusUpdate(msg, ProgressBarStyle.Continuous, _info);
}
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
}
}
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();
}
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();
}
void processFile(string filename, Config config, ReaderList readers)
{
if (LogUpdate != null)
{
LogUpdate("Opening file...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Opening file...", ProgressBarStyle.Marquee, _info);
}
// read in data file
using (var msdList = new MSDataList())
{
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
{
throw new ArgumentException("Output filepath is the same as input filepath");
}
if (LogUpdate != null)
{
LogUpdate("Calculating SHA1 checksum...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
}
// only one thread
lock (calculateSHA1Mutex)
MSDataFile.calculateSHA1Checksums(msd);
if (LogUpdate != null)
{
LogUpdate("Processing...", _info);
}
if (StatusUpdate != null)
{
StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
}
SpectrumListFactory.wrap(msd, config.Filters);
if (StatusUpdate != null && msd.run.spectrumList != null)
{
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
}
// write out the new data file
IterationListenerRegistry ilr = null;
ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
}
}
}
void processFile(string filename, Config config, ReaderList readers)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...",filename);
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
readers.read(filename, msdList);
foreach (var msd in msdList)
{
var outputFilename = config.outputFilename(filename, msd);
if (filename == outputFilename)
throw new ArgumentException("Output filepath is the same as input filepath");
if (StatusUpdate != null) StatusUpdate("Waiting...", ProgressBarStyle.Marquee, _info);
// only one thread
lock (calculateSHA1Mutex)
{
if (LogUpdate != null) LogUpdate("Calculating SHA1 checksum...", _info);
if (StatusUpdate != null) StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
MSDataFile.calculateSHA1Checksums(msd);
}
if (LogUpdate != null) LogUpdate("Processing...", _info);
if (StatusUpdate != null) StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info);
SpectrumListFactory.wrap(msd, config.Filters);
if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty())
{
if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty())
{
msg = "Note: input contains only chromatogram data.";
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_MZ5:
case MSDataFile.Format.Format_mzML:
break;
default:
msg += " The selected output format can only represent spectra. Consider using mzML instead.";
break;
}
}
else
msg = "Note: input contains no spectra or chromatogram data.";
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
}
if (StatusUpdate != null && msd.run.spectrumList != null)
StatusUpdate(String.Format("Processing ({0} of {1})",
DataGridViewProgressCell.MessageSpecialValue.CurrentValue,
DataGridViewProgressCell.MessageSpecialValue.Maximum),
ProgressBarStyle.Continuous, _info);
// write out the new data file
var ilr = new IterationListenerRegistry();
ilr.addListener(this, 100);
msg = String.Format("Writing \"{0}\"...", outputFilename);
if (LogUpdate != null) LogUpdate(msg, _info);
if (StatusUpdate != null) StatusUpdate(msg, ProgressBarStyle.Marquee, _info);
MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
}
}
private void loadRefSeqGeneMetadata()
{
#region Check for updated gene2protein database and download it
if (!File.Exists(Path.Combine(Application.StartupPath, "gene2protein.db3")))
throw new Exception("missing gene2protein.db3 mapping file");
/*string g2pTimestamp = null;
string g2pPath = Path.Combine(Application.UserAppDataPath, "gene2protein.db3");
string g2pPathAlternate = Path.Combine(Application.StartupPath, "gene2protein.db3");
var copyUserToAlternate = new ProcessStartInfo("cmd.exe", String.Format("/C copy /Y \"{0}\" \"{1}\"", g2pPath, g2pPathAlternate));
copyUserToAlternate.CreateNoWindow = true;
if (!File.Exists(g2pPath) && File.Exists(g2pPathAlternate))
File.Copy(g2pPathAlternate, g2pPath);
else if (File.Exists(g2pPath) && !File.Exists(g2pPathAlternate))
{
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
if (File.Exists(g2pPath))
{
// if the file exists, check its timestamp and compare it to the timestamp on the server
using (var con = new SQLiteConnection(@"Data Source=" + g2pPath + ";Version=3"))
{
try
{
con.Open();
g2pTimestamp = con.ExecuteQuery("SELECT Timestamp FROM About").Single().GetString(0);
}
catch (Exception e)
{
throw new Exception("error getting timestamp of current gene2protein database (\"" + g2pPath + "\"): " + e.Message, e);
}
}
string g2pURL = "http://fenchurch.mc.vanderbilt.edu/bin/g2p";
string g2pTimestampURL = String.Format("{0}/G2P_TIMESTAMP", g2pURL);
string latestTimestamp;
lock (Program.WebClient)
{
latestTimestamp = Program.WebClient.DownloadString(g2pTimestampURL).Trim();
}
if (g2pTimestamp.CompareTo(latestTimestamp) < 0)
{
Invoke(new MethodInvoker(() =>
{
var form = new NewVersionForm("RefSeq Gene to Protein Database",
g2pTimestamp,
latestTimestamp,
String.Empty)
{
Owner = this,
StartPosition = FormStartPosition.CenterParent
};
if (form.ShowDialog() == DialogResult.Yes)
{
var oldG2Ptime = File.GetLastWriteTimeUtc(g2pPath);
string backupG2Pname = String.Format("{0}.{1}.bak", g2pPath, oldG2Ptime.ToString("yyyyMMddHHmm"));
try
{
if (!File.Exists(backupG2Pname))
File.Copy(g2pPath, backupG2Pname);
File.Delete(g2pPath);
string g2pDatabaseURL = String.Format("{0}/gene2protein.db3", g2pURL);
lock (Program.WebClient)
{
Program.WebClient.DownloadFile(g2pDatabaseURL, g2pPath);
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
g2pTimestamp = latestTimestamp;
}
catch (Exception)
{
if (!File.Exists(g2pPath))
File.Move(backupG2Pname, g2pPath);
}
}
else
g2pTimestamp = null; // no update
}));
}
else
g2pTimestamp = null; // no update
}
else // downloading database for the first time (or it has been deleted)
{
string g2pURL = "http://fenchurch.mc.vanderbilt.edu/bin/g2p";
string g2pDatabaseURL = String.Format("{0}/gene2protein.db3", g2pURL);
lock (Program.WebClient)
{
Program.WebClient.DownloadFile(g2pDatabaseURL, g2pPath);
var p = Process.Start(copyUserToAlternate);
p.WaitForExit();
if (p.ExitCode == 1)
MessageBox.Show("Unable to copy gene2protein.db3 from user-specific path to application path:\r\n" +
Path.GetDirectoryName(g2pPath) +
"\r\nto\r\n" +
Path.GetDirectoryName(g2pPathAlternate),
"Unable to copy");
}
}*/
#endregion
if (session == null)
return;
try
{
clearSession();
var ilr = new IterationListenerRegistry();
ilr.addListener(progressMonitor.GetIterationListenerProxy(), 1);
Embedder.EmbedGeneMetadata(Text, ilr);
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "embedding gene metadata failed");
}
OpenFiles(new List<string> { Text }, null);
}
public ProgressForm(IEnumerable<string> taskNames, IterationListenerRegistry ilr)
{
InitializeComponent();
_progressCellByTaskName = new Dictionary<string, DataGridViewProgressCell>();
_textBoxLogByTaskName = new Dictionary<string, TextBox>();
_lastMessageByTaskName = new Dictionary<string, string>();
_rowByTaskName = new Dictionary<string, DataGridViewRow>();
_tasksDone = 0;
_ilr = ilr;
_ilProxy = new IterationListenerProxy() { form = this };
_ilr.addListener(_ilProxy, 1000);
var boxShown = false;
foreach (var task in taskNames)
{
var textBox = _textBoxLogByTaskName[task] = new TextBox
{
Text = String.Format("{0}{1}{0}Starting...{0}",
Environment.NewLine,
new string('-', 30)),
Dock = DockStyle.Fill,
Multiline = true,
ScrollBars = ScrollBars.Vertical
};
if (boxShown)
textBox.Visible = false;
else
{
textBox.Visible = true;
boxShown = true;
}
ProgressSplit.Panel2.Controls.Add(textBox);
JobDataView.Rows.Add(task, 0);
var row = JobDataView.Rows[JobDataView.Rows.Count - 1];
row.Tag = textBox;
_rowByTaskName[task] = row;
_progressCellByTaskName[task] = row.Cells[1] as DataGridViewProgressCell;
_progressCellByTaskName[task].Text = "waiting";
}
}
