public void QueueWork(Config config)
{
if (StatusUpdate != null) StatusUpdate("Waiting...", ProgressBarStyle.Continuous, _info);
_canceled = false;
lock (_workQueue)
_workQueue.Enqueue(new KeyValuePair<MainLogic, Config>(this, config));
}
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);
}
}
}
/// <summary>
/// Processes files, returns number of failed files
/// </summary>
/// <param name="config"></param>
/// <returns></returns>
int Go(Config config)
{
var readers = ReaderList.FullReaderList;
var failedFileCount = 0;
foreach (var it in config.Filenames)
{
try
{
processFile(it, config, readers);
}
catch (Exception e)
{
_errorMessage = e.ToString();
failedFileCount++;
if (LogUpdate == null)
throw;
}
}
return failedFileCount;
}
public Config ParseCommandLine(string outputFolder, string argv)
{
var config = new Config(outputFolder);
string filelistFilename = null;
string configFilename = null;
var formatText = false;
var formatMzMl = false;
var formatMzXml = false;
var formatMz5 = false;
var formatMgf = false;
var formatMs1 = false;
var formatCms1 = false;
var formatMs2 = false;
var formatCms2 = false;
var precision32 = false;
var precision64 = false;
var noindex = false;
var zlib = false;
var gzip = false;
var commandList = argv.Split('|');
for (var x = 0; x < commandList.Length; x++)
{
switch (commandList[x])
{
case "--filelist":
case "-f":
x++;
filelistFilename = commandList[x];
break;
case "--config":
case "-c":
x++;
configFilename = commandList[x];
break;
case "--ext":
case "-e":
x++;
config.Extension = commandList[x];
break;
case "--mzML":
formatMzMl = true;
break;
case "--mzXML":
formatMzXml = true;
break;
case "--mz5":
formatMz5 = true;
break;
case "--mgf":
formatMgf = true;
break;
case "--text":
formatText = true;
break;
case "--ms1":
formatMs1 = true;
break;
case "--cms1":
formatCms1 = true;
break;
case "--ms2":
formatMs2 = true;
break;
case "--cms2":
formatCms2 = true;
break;
case "--64":
precision64 = true;
break;
case "--32":
precision32 = true;
break;
case "--noindex":
noindex = true;
break;
case "--contactinfo":
case "-i":
x++;
config.ContactFilename = commandList[x];
break;
case "--zlib":
case "-z":
zlib = true;
break;
case "--gzip":
case "-g":
gzip = true;
break;
case "--filter":
x++;
config.Filters.Add(commandList[x]);
break;
case "--numpressPic":
config.WriteConfig.numpressPic = true;
break;
case "--numpressLinear":
config.WriteConfig.numpressLinear = true;
break;
case "--numpressSlof":
config.WriteConfig.numpressLinear = true;
break;
default:
config.Filenames.Add(commandList[x]);
break;
}
}
#region Parse config file if required
if (!string.IsNullOrEmpty(configFilename))
{
var fileIn = new StreamReader(configFilename);
var entirefile = fileIn.ReadToEnd().Replace('=', ' ').Replace(Environment.NewLine, " ");
fileIn.Close();
commandList = entirefile.Split();
for (var x = 0; x < commandList.Length; x++)
{
switch (commandList[x])
{
case "--filelist":
case "-f":
x++;
filelistFilename = commandList[x];
break;
case "--outdir":
case "-o":
x++;
config.OutputPath = commandList[x];
break;
case "--ext":
case "-e":
x++;
config.Extension = commandList[x];
break;
case "--mzML":
formatMzMl = true;
break;
case "--mzXML":
formatMzXml = true;
break;
case "--mgf":
formatMgf = true;
break;
case "--text":
formatText = true;
break;
case "--ms1":
formatMs1 = true;
break;
case "--cms1":
formatCms1 = true;
break;
case "--ms2":
formatMs2 = true;
break;
case "--cms2":
formatCms2 = true;
break;
case "--64":
precision64 = true;
break;
case "--32":
precision32 = true;
break;
case "--noindex":
noindex = true;
break;
case "--contactinfo":
case "-i":
x++;
config.ContactFilename = commandList[x];
break;
case "--zlib":
case "-z":
zlib = true;
break;
case "--gzip":
case "-g":
gzip = true;
break;
case "--filter":
x++;
config.Filters.Add(commandList[x]);
break;
}
}
}
#endregion
// parse filelist if required
if (!string.IsNullOrEmpty(filelistFilename))
{
var fileIn = new StreamReader(filelistFilename);
while (!fileIn.EndOfStream)
{
var filename = fileIn.ReadLine();
if (!string.IsNullOrEmpty(filename))
config.Filenames.Add(filename);
}
fileIn.Close();
}
// check stuff
if (config.Filenames.Count == 0)
throw new Exception("[msconvert] No files specified.");
var count = (formatText ? 1 : 0)
+ (formatMzMl ? 1 : 0)
+ (formatMzXml ? 1 : 0)
+ (formatMz5 ? 1 : 0)
+ (formatMgf ? 1 : 0)
+ (formatMs1 ? 1 : 0)
+ (formatCms1 ? 1 : 0)
+ (formatMs2 ? 1 : 0)
+ (formatCms2 ? 1 : 0);
if (count > 1) throw new Exception("[msconvert] Multiple format flags specified.");
if (formatText) config.WriteConfig.format = MSDataFile.Format.Format_Text;
if (formatMzMl) config.WriteConfig.format = MSDataFile.Format.Format_mzML;
if (formatMzXml) config.WriteConfig.format = MSDataFile.Format.Format_mzXML;
if (formatMz5) config.WriteConfig.format = MSDataFile.Format.Format_MZ5;
if (formatMgf) config.WriteConfig.format = MSDataFile.Format.Format_MGF;
if (formatMs1) config.WriteConfig.format = MSDataFile.Format.Format_MS1;
if (formatCms1) config.WriteConfig.format = MSDataFile.Format.Format_CMS1;
if (formatMs2) config.WriteConfig.format = MSDataFile.Format.Format_MS2;
if (formatCms2) config.WriteConfig.format = MSDataFile.Format.Format_CMS2;
config.WriteConfig.gzipped = gzip; // if true, file is written as .gz
if (String.IsNullOrEmpty(config.Extension))
{
switch (config.WriteConfig.format)
{
case MSDataFile.Format.Format_Text:
config.Extension = ".txt";
break;
case MSDataFile.Format.Format_mzML:
config.Extension = ".mzML";
break;
case MSDataFile.Format.Format_mzXML:
config.Extension = ".mzXML";
break;
case MSDataFile.Format.Format_MZ5:
config.Extension = ".mz5";
break;
case MSDataFile.Format.Format_MGF:
config.Extension = ".mgf";
break;
case MSDataFile.Format.Format_MS1:
config.Extension = ".ms1";
break;
case MSDataFile.Format.Format_CMS1:
config.Extension = ".cms1";
break;
case MSDataFile.Format.Format_MS2:
config.Extension = ".ms2";
break;
case MSDataFile.Format.Format_CMS2:
config.Extension = ".cms2";
break;
default:
throw new Exception("[msconvert] Unsupported format.");
}
if (config.WriteConfig.gzipped)
{
config.Extension += ".gz";
}
}
// precision defaults
config.WriteConfig.precision = MSDataFile.Precision.Precision_64;
// handle precision flags
if (precision32 && precision64)
throw new Exception("[msconvert] Incompatible precision flags.");
if (precision32)
{
config.WriteConfig.precision = MSDataFile.Precision.Precision_32;
}
else if (precision64)
{
config.WriteConfig.precision = MSDataFile.Precision.Precision_64;
}
// other flags
if (noindex)
config.WriteConfig.indexed = false;
if (zlib)
config.WriteConfig.compression = MSDataFile.Compression.Compression_Zlib;
return config;
}
