public MaxQuantMgfDistiller(string[] sourceFiles, ITitleParser parser, bool singleResult, string singleResultFilename)
{
this.sourceFiles = sourceFiles;
this.parser = parser;
this.singleResult = singleResult;
this.singleResultFilename = singleResultFilename;
}
public SequestFilename GetValue(string obj)
{
for (int i = 0; i < parsers.Count; i++)
{
ITitleParser parser = parsers[i];
try
{
SequestFilename result = parser.GetValue(obj);
if (i != 0 && moveCount < 10)
{
parsers.Remove(parser);
parsers.Insert(0, parser);
moveCount++;
}
return(result);
}
catch (Exception)
{
}
}
return(MascotUtils.ParseTitle(obj, 2));
}
public XTandemSpectrumXmlParser(ITitleParser parser)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
this.TitleParser = parser;
}
public AbstractMzIdentParser(ITitleParser parser, bool extractRank2 = false)
{
this.TitleParser = parser;
this.ExtractRank2 = extractRank2;
}
public PFindSpectrumParser(ITitleParser parser)
{
this.TitleParser = parser;
}
public OmssaOmxParser(ITitleParser parser)
{
this.TitleParser = parser;
}
public MaxQuantAplFormat(ITitleParser parser)
{
this.parser = parser;
}
public Mgf2Ms2Processor(String targetFile, ITitleParser parser)
{
this.targetFile = targetFile;
this.parser = parser;
}
public MyriMatchMzIdentParser(ITitleParser parser, bool extractRank2) : base(parser, extractRank2)
{
}
public MSGFMzIdentParser(ITitleParser parser) : base(parser)
{
}
public MSGFMzIdentParser(ITitleParser parser, bool extractRank2) : base(parser, extractRank2)
{
}
public PNovoParser(ITitleParser parser)
{
this.parser = parser;
this.ModificationCharMap = new Dictionary <string, char>();
}
public UpdatePepXmlModificationProcessor(ITitleParser parser, IEnumerable <string> sourceFiles)
{
this.parser = parser;
this.sourceFiles = sourceFiles.ToList();
}
public MyriMatchMzIdentParser(ITitleParser parser) : base(parser)
{
}
public UpdateMascotDatTitleFormatProcessor(ITitleParser parser, IEnumerable <string> sourceFiles)
{
this.parser = parser;
this.sourceFiles = sourceFiles.ToList();
}
private static Dictionary <string, PeakList <Peak> > ReadPeakMap(string file, ITitleParser parser)
{
var reader = new MascotGenericFormatReader <Peak>();
List <PeakList <Peak> > hList = reader.ReadFromFile(file);
return(hList.ToDictionary(m =>
{
var filename = parser.GetValue(m.Annotations[MascotGenericFormatConstants.TITLE_TAG] as string);
if (string.IsNullOrEmpty(m.Experimental))
{
m.Experimental = filename.Experimental;
}
if (m.FirstScan == 0)
{
m.FirstScan = filename.FirstScan;
}
if (filename.Charge > 0)
{
m.PrecursorCharge = filename.Charge;
}
return filename.FirstScan.ToString();
}));
}
public MascotDatSpectrumParser(ITitleParser parser)
{
this.TitleParser = parser;
}
