public override IEnumerable <string> Process()
{
var result = new List <string>();
var titleParser = options.GetTitleParser();
var writer = new MascotGenericFormatWriter <Peak>();
Progress.SetRange(0, options.InputFiles.Count);
int count = 0;
foreach (var file in options.InputFiles)
{
count++;
string resultFilename = options.GetOutputFile(file);
Progress.SetMessage("Processing {0}/{1} : {2} ...", count, options.InputFiles.Count, file);
var tempFile = resultFilename + ".tmp";
using (var sw = new StreamWriter(tempFile))
{
sw.WriteLine("###ShiftMass={0:0.#}", options.ShiftMass);
sw.WriteLine("###ShiftScan={0}", options.ShiftScan);
sw.WriteLine();
using (var sr = new StreamReader(new FileStream(file, FileMode.Open)))
{
var iter = new MascotGenericFormatIterator <Peak>(sr);
while (iter.HasNext())
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
var pkl = iter.Next();
UpdatePrecursor(titleParser, pkl, options.ShiftMass, options.ShiftScan);
writer.Write(sw, pkl);
}
}
}
if (File.Exists(resultFilename))
{
File.Delete(resultFilename);
}
File.Move(tempFile, resultFilename);
result.Add(resultFilename);
}
Progress.End();
return(result);
}
public List <PeakList <T> > ReadFromFile(string filename)
{
var fi = new FileInfo(filename);
if (!fi.Exists)
{
throw new FileNotFoundException("Cannot find the file " + filename);
}
String experimental = FileUtils.ChangeExtension(fi.Name, "");
var result = new List <PeakList <T> >();
var sr = new StreamReader(new FileStream(filename, FileMode.Open));
try
{
var iter = new MascotGenericFormatIterator <T>(sr);
while (iter.HasNext())
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
var pkl = iter.Next();
if (pkl.Experimental == null || pkl.Experimental.Length == 0)
{
pkl.Experimental = experimental;
}
result.Add(pkl);
}
}
finally
{
sr.Close();
}
return(result);
}