public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
ReaderList.FullReaderList.read(filepath, msdList, readerConfig);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
if (!File.Exists(filepath) && !Directory.Exists(filepath)) // Some mass spec "files" are really directory structures
{
throw new FileNotFoundException("Filepath not found: " + filepath, filepath);
}
ReaderList.FullReaderList.read(filepath, msdList, GetReaderConfig());
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
private SourceInfo[] getSourceInfo(FileInfo fileInfo, bool getDetails)
{
var sourceInfoList = new List <SourceInfo>();
sourceInfoList.Add(new SourceInfo());
sourceInfoList[0].type = getSourceType(fileInfo);
sourceInfoList[0].name = fileInfo.Name;
sourceInfoList[0].hasDetails = getDetails;
sourceInfoList[0].size = (UInt64)fileInfo.Length;
sourceInfoList[0].dateModified = fileInfo.LastWriteTime;
if (sourceInfoList[0].type != String.Empty)
{
if (!getDetails)
{
return(sourceInfoList.ToArray());
}
try
{
ReaderList readerList = ReaderList.FullReaderList;
var readerConfig = new ReaderConfig
{
simAsSpectra = Properties.Settings.Default.SimAsSpectra,
srmAsSpectra = Properties.Settings.Default.SrmAsSpectra,
combineIonMobilitySpectra = Properties.Settings.Default.CombineIonMobilitySpectra,
ignoreZeroIntensityPoints = Properties.Settings.Default.IgnoreZeroIntensityPoints,
acceptZeroLengthSpectra = Properties.Settings.Default.AcceptZeroLengthSpectra,
allowMsMsWithoutPrecursor = false
};
MSDataList msInfo = new MSDataList();
readerList.read(fileInfo.FullName, msInfo, readerConfig);
foreach (MSData msData in msInfo)
{
SourceInfo sourceInfo = new SourceInfo();
sourceInfo.type = sourceInfoList[0].type;
sourceInfo.name = sourceInfoList[0].name;
if (msInfo.Count > 1)
{
sourceInfo.name += " (" + msData.run.id + ")";
}
sourceInfo.populateFromMSData(msData);
sourceInfoList.Add(sourceInfo);
}
} catch
{
sourceInfoList[0].spectra = 0;
sourceInfoList[0].type = "Invalid " + sourceInfoList[0].type;
}
foreach (SourceInfo sourceInfo in sourceInfoList)
{
sourceInfo.size = (UInt64)fileInfo.Length;
sourceInfo.dateModified = fileInfo.LastWriteTime;
}
return(sourceInfoList.ToArray());
}
return(null);
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(filepath, msdList);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
}
private SourceInfo[] getSourceInfo(FileInfo fileInfo, bool getDetails)
{
var sourceInfoList = new List <SourceInfo>();
sourceInfoList.Add(new SourceInfo());
sourceInfoList[0].type = getSourceType(fileInfo);
sourceInfoList[0].name = fileInfo.Name;
sourceInfoList[0].hasDetails = getDetails;
sourceInfoList[0].size = (UInt64)fileInfo.Length;
sourceInfoList[0].dateModified = fileInfo.LastWriteTime;
if (sourceInfoList[0].type != String.Empty)
{
if (!getDetails)
{
return(sourceInfoList.ToArray());
}
try
{
ReaderList readerList = ReaderList.FullReaderList;
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
MSDataList msInfo = new MSDataList();
readerList.read(fileInfo.FullName, msInfo, readerConfig);
foreach (MSData msData in msInfo)
{
SourceInfo sourceInfo = new SourceInfo();
sourceInfo.type = sourceInfoList[0].type;
sourceInfo.name = sourceInfoList[0].name;
if (msInfo.Count > 1)
{
sourceInfo.name += " (" + msData.run.id + ")";
}
sourceInfo.populateFromMSData(msData);
sourceInfoList.Add(sourceInfo);
}
} catch
{
sourceInfoList[0].spectra = 0;
sourceInfoList[0].type = "Invalid " + sourceInfoList[0].type;
}
foreach (SourceInfo sourceInfo in sourceInfoList)
{
sourceInfo.size = (UInt64)fileInfo.Length;
sourceInfo.dateModified = fileInfo.LastWriteTime;
}
return(sourceInfoList.ToArray());
}
return(null);
}
public SpectrumSource(string filepath)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(filepath, msdList);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
setInputFileWaitHandle = new EventWaitHandle(false, EventResetMode.ManualReset);
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
* Thread setInputFileThread = new Thread( setInputFileDelegate );
*
* setInputFileThread.Start( (object) filepath );*/
}
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);
}
}
}
void processFile(string filename, Config config, ReaderList readers, Map <string, int> usedOutputFilenames)
{
// read in data file
using (var msdList = new MSDataList())
{
string msg = String.Format("Opening file \"{0}\" for read...", filename);
var stripCredentialsMatch = Regex.Match(filename, "https?://([^:]+:[^@]+@).*", RegexOptions.CultureInvariant | RegexOptions.IgnoreCase);
if (stripCredentialsMatch.Success)
{
msg = msg.Replace(stripCredentialsMatch.Groups[1].Value, "");
}
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(msg, ProgressBarStyle.Marquee, _info);
readers.read(filename, msdList, config.ReaderConfig);
foreach (var msd in msdList)
{
try
{
var outputFilename = config.outputFilename(filename, msd);
string deduplicatedFilename = outputFilename;
StatusUpdate?.Invoke("Waiting...", ProgressBarStyle.Marquee, _info);
// only one thread
lock (_calculateSHA1Mutex)
{
// if output name is same as input name, add a suffix
if (filename == outputFilename)
{
++usedOutputFilenames[outputFilename];
}
if (usedOutputFilenames.Contains(deduplicatedFilename))
{
deduplicatedFilename = deduplicatedFilename.Replace(Path.GetExtension(outputFilename), String.Format(" ({0}).{1}", usedOutputFilenames[outputFilename] + 1, Path.GetExtension(outputFilename)));
}
++usedOutputFilenames[outputFilename];
LogUpdate?.Invoke("Calculating SHA1 checksum...", _info);
StatusUpdate?.Invoke("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info);
MSDataFile.calculateSHA1Checksums(msd);
}
var ilr = new IterationListenerRegistry();
ilr.addListenerWithTimer(this, 1);
LogUpdate?.Invoke("Processing...", _info);
StatusUpdate?.Invoke("Processing...", ProgressBarStyle.Marquee, _info);
SpectrumListFactory.wrap(msd, config.Filters, ilr);
config.WriteConfig.useWorkerThreads = msd.run.spectrumList.benefitsFromWorkerThreads();
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.";
}
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(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
msg = String.Format("Writing \"{0}\"...", deduplicatedFilename);
LogUpdate?.Invoke(msg, _info);
StatusUpdate?.Invoke(msg, ProgressBarStyle.Continuous, _info);
MSDataFile.write(msd, deduplicatedFilename, config.WriteConfig, ilr);
ilr.removeListener(this);
}
finally
{
msd.Dispose();
}
}
}
}
public void Open(string fileName, int sampleIndex)
{
if (_currentSampleIndex != sampleIndex || _currentFileName != fileName)
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read(fileName, msdList);
_dataFile = msdList[0];
_run = _dataFile.run;
_currentFileName = fileName;
_currentSampleIndex = sampleIndex;
spectrumCache = new SpectrumCache();
ticGenerator = new TicGenerator(_run, spectrumCache);
xicGenerator = new XicGenerator(_run, spectrumCache);
spectrumExtractor = new SpectrumExtractor(_run, spectrumCache);
averagedSpectrumExtractor = new AveragedSpectrumExtractor(_run, spectrumCache);
}
}
public SpectrumSource( string filepath )
{
MSDataList msdList = new MSDataList();
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
ReaderList.FullReaderList.read(filepath, msdList, readerConfig);
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
// create dummy spectrum/chromatogram list to simplify logic
msDataFile.run.spectrumList = msDataFile.run.spectrumList ?? new SpectrumListSimple();
msDataFile.run.chromatogramList = msDataFile.run.chromatogramList ?? new ChromatogramListSimple();
setInputFileWaitHandle = new EventWaitHandle( false, EventResetMode.ManualReset );
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
Thread setInputFileThread = new Thread( setInputFileDelegate );
setInputFileThread.Start( (object) filepath );*/
}
private SourceInfo[] getSourceInfo( FileInfo fileInfo, bool getDetails )
{
var sourceInfoList = new List<SourceInfo>();
sourceInfoList.Add( new SourceInfo() );
sourceInfoList[0].type = getSourceType( fileInfo );
sourceInfoList[0].name = fileInfo.Name;
sourceInfoList[0].hasDetails = getDetails;
sourceInfoList[0].size = (UInt64) fileInfo.Length;
sourceInfoList[0].dateModified = fileInfo.LastWriteTime;
if( sourceInfoList[0].type != String.Empty )
{
if( !getDetails )
return sourceInfoList.ToArray();
try
{
ReaderList readerList = ReaderList.FullReaderList;
var readerConfig = new ReaderConfig
{
simAsSpectra = Program.SimAsSpectra,
srmAsSpectra = Program.SrmAsSpectra
};
MSDataList msInfo = new MSDataList();
readerList.read( fileInfo.FullName, msInfo, readerConfig );
foreach( MSData msData in msInfo )
{
SourceInfo sourceInfo = new SourceInfo();
sourceInfo.type = sourceInfoList[0].type;
sourceInfo.name = sourceInfoList[0].name;
if( msInfo.Count > 1 )
sourceInfo.name += " (" + msData.run.id + ")";
sourceInfo.populateFromMSData( msData );
sourceInfoList.Add( sourceInfo );
}
} catch
{
sourceInfoList[0].spectra = 0;
sourceInfoList[0].type = "Invalid " + sourceInfoList[0].type;
}
foreach( SourceInfo sourceInfo in sourceInfoList )
{
sourceInfo.size = (UInt64) fileInfo.Length;
sourceInfo.dateModified = fileInfo.LastWriteTime;
}
return sourceInfoList.ToArray();
}
return null;
}
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);
}
}
}
public SpectrumSource( string filepath )
{
MSDataList msdList = new MSDataList();
ReaderList.FullReaderList.read( filepath, msdList );
msDataFile = msdList[0];
//msDataFile = new MSDataFile(filepath);
sourceFilepath = filepath;
setInputFileWaitHandle = new EventWaitHandle( false, EventResetMode.ManualReset );
/*setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile );
Thread setInputFileThread = new Thread( setInputFileDelegate );
setInputFileThread.Start( (object) filepath );*/
}
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);
}
}
}