public override IEnumerable <string> Process(string filename)
{
var parser = new OutParser();
string resultFilename;
if (null == this.targetDir)
{
resultFilename = FileUtils.ChangeExtension(filename, ".xml");
}
else
{
resultFilename = targetDir + "/" + FileUtils.ChangeExtension(new FileInfo(filename).Name, ".xml");
}
using (PepXmlWriter writer = new PepXmlWriter("out"))
{
writer.Open(resultFilename);
writer.OpenMsmsRunSummary(filename);
SequestParam sp = new SequestParamFile().ReadFromFile(filename);
writer.WriteSequestParam(sp);
using (var reader = new OutsReader(filename))
{
int totalCount = reader.FileCount;
Progress.SetRange(0, totalCount);
int currentCount = 0;
while (reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
List <string> contents = reader.NextContent();
IIdentifiedSpectrum sph = parser.Parse(contents);
if (sph == null)
{
continue;
}
writer.WriteSequestPeptideHit(sph);
currentCount++;
Progress.SetPosition(currentCount);
}
Progress.SetPosition(totalCount);
}
writer.CloseMsmsRunSummary();
}
return(new[] { resultFilename });
}
private void ExtractFileByPeptide(OutsReader reader, Dictionary <string, IIdentifiedSpectrum> outFilenamePeptideMap, string toDirectory)
{
Progress.SetRange(0, 1, reader.FileCount);
int count = 0;
while (outFilenamePeptideMap.Count > 0 && reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
string filename = reader.NextFilename;
if (outFilenamePeptideMap.ContainsKey(filename))
{
List <string> content = reader.NextContent();
IIdentifiedSpectrum sph = outFilenamePeptideMap[filename];
IIdentifiedSpectrum parsed = parser.Parse(content);
if (sph.Sequence.Equals(parsed.Sequence))
{
string targetFilename = toDirectory + "/" + filename;
using (StreamWriter sw = new StreamWriter(targetFilename))
{
foreach (string line in content)
{
sw.WriteLine(line);
}
}
outFilenamePeptideMap.Remove(filename);
}
}
else
{
reader.SkipNextContent();
}
Progress.SetPosition(0, count++);
}
Progress.SetPosition(0, reader.FileCount);
}
