/// <summary>
/// Run Monocle on the files indicated in the Processor
/// </summary>
public async void Run()
{
tokenSource = new CancellationTokenSource();
CancellationToken token = tokenSource.Token;
await Task.Run(() =>
{
token.ThrowIfCancellationRequested();
try
{
int filesCompleted = 0;
foreach (string newFile in files.FileList)
{
CurrentProgress = CalculateProgress(1, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Started);
token.ThrowIfCancellationRequested();
IScanReader reader = ScanReaderFactory.GetReader(newFile);
reader.Open(newFile);
ScanFileHeader header = reader.GetHeader();
header.FileName = Path.GetFileName(newFile);
var Scans = new List <Monocle.Data.Scan>();
foreach (Scan scan in reader)
{
token.ThrowIfCancellationRequested();
Scans.Add(scan);
}
reader.Close();
CurrentProgress = CalculateProgress(2, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Read);
token.ThrowIfCancellationRequested();
if (!ConvertOnly)
{
// Start Run across Scans
Monocle.Monocle.Run(ref Scans, monocleOptions);
CurrentProgress = CalculateProgress(3, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Processed);
token.ThrowIfCancellationRequested();
}
string outputFilePath = Path.Combine(Path.GetDirectoryName(newFile), Path.GetFileNameWithoutExtension(newFile) +
"_monocle." +
monocleOptions.OutputFileType.ToString());
ScanWriterFactory.MakeTargetFileName(newFile, monocleOptions.OutputFileType);
IScanWriter writer = ScanWriterFactory.GetWriter(monocleOptions.OutputFileType);
writer.Open(outputFilePath);
writer.WriteHeader(header);
foreach (Scan scan in Scans)
{
token.ThrowIfCancellationRequested();
writer.WriteScan(scan);
}
writer.Close();
CurrentProgress = CalculateProgress(4, filesCompleted, files.FileList.Count);
TrackProcess(outputFilePath, CurrentProgress, RunStatus.Written);
token.ThrowIfCancellationRequested();
// Clear data
EmptyScans(Scans);
filesCompleted++;
CurrentProgress = CalculateProgress(4, filesCompleted, files.FileList.Count);
TrackProcess(outputFilePath, CurrentProgress, RunStatus.Finished);
}
AllFilesFinished(true);
}
catch (Exception ex)
{
Debug.WriteLine("File processing failed: " + ex);
}
});
}
static void Main(string[] args)
{
var parser = new CliOptionsParser();
MakeMonoOptions options = parser.Parse(args);
MonocleOptions monocleOptions = new MonocleOptions
{
AveragingVector = options.AveragingVector,
Charge_Detection = options.ChargeDetection,
Charge_Range = new ChargeRange(options.ChargeRange),
MS_Level = options.MS_Level,
Number_Of_Scans_To_Average = options.NumOfScans,
WriteDebugString = options.WriteDebug,
OutputFileType = options.OutputFileType,
ConvertOnly = options.ConvertOnly,
SkipMono = options.SkipMono,
ChargeRangeUnknown = new ChargeRange(options.ChargeRangeUnknown),
ForceCharges = options.ForceCharges,
UseMostIntense = options.UseMostIntense
};
SetupLogger(options.RunQuiet, options.WriteDebug);
try
{
log.Info("Starting Processing.");
string file = options.InputFilePath;
IScanReader reader = ScanReaderFactory.GetReader(file);
reader.Open(file);
var header = reader.GetHeader();
header.FileName = Path.GetFileName(file);
log.Info("Reading scans: " + file);
List <Scan> Scans = new List <Scan>();
foreach (Scan scan in reader)
{
Scans.Add(scan);
}
if (!monocleOptions.ConvertOnly)
{
log.Info("Starting monoisotopic assignment.");
Monocle.Monocle.Run(ref Scans, monocleOptions);
}
string outputFilePath = options.OutputFilePath.Trim();
if (outputFilePath.Length == 0)
{
outputFilePath = ScanWriterFactory.MakeTargetFileName(file, monocleOptions.OutputFileType);
}
log.Info("Writing output: " + outputFilePath);
IScanWriter writer = ScanWriterFactory.GetWriter(monocleOptions.OutputFileType);
writer.Open(outputFilePath);
writer.WriteHeader(header);
foreach (Scan scan in Scans)
{
writer.WriteScan(scan);
}
writer.Close();
log.Info("Done.");
}
catch (Exception e)
{
log.Error("An error occurred.");
log.Debug(e.GetType().ToString());
log.Debug(e.Message);
log.Debug(e.ToString());
}
}