public Raw2MgfProcessor(MultipleRaw2MgfOptions options) : base(options)
{
this.options = options;
this.Writer = options.GetMGFWriter();
this.swMap = new Dictionary <string, StreamWriter>();
this.outputFiles = new List <string>();
}
public MascotGenericFormatWriter <Peak> GetMGFWriter()
{
var result = new MascotGenericFormatWriter <Peak>()
{
TitleFormat = MascotTitleFactory.FindTitleOrDefault(MascotTitleName)
};
result.Comments.Clear();
result.Comments.Add("Converter=" + ConverterName);
result.Comments.Add("ConverterVersion=" + ConverterVersion);
result.Comments.Add("DefaultCharges=" + DefaultCharges.ToString());
result.Comments.Add("ProductIonPPM=" + ProductIonPPM.ToString());
result.DefaultCharges = this.DefaultCharges.DefaultCharges;
return(result);
}
public override IEnumerable <string> Process(string fileName)
{
double offsetPPM;
if (!FindOffset(fileName, out offsetPPM))
{
return(new string[] { });
}
string resultFilename = new FileInfo(targetDir + "\\" + new FileInfo(fileName).Name).FullName;
var writer = new MascotGenericFormatWriter <Peak>();
using (StreamReader sr = new StreamReader(new FileStream(fileName, FileMode.Open)))
{
var iter = new MascotGenericFormatIterator <Peak>(sr);
using (StreamWriter sw = new StreamWriter(resultFilename))
{
while (iter.HasNext())
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
if (IsLoopStopped)
{
return(new string[] { });
}
var pkl = iter.Next();
pkl.PrecursorMZ = pkl.PrecursorMZ + PrecursorUtils.ppm2mz(pkl.PrecursorMZ, offsetPPM);
writer.Write(sw, pkl);
}
}
}
return(new List <string>(new[] { resultFilename }));
}
public override IEnumerable <string> Process(string targetFile)
{
var hMap = ReadPeakMap(option.HeaderFile, option.HeaderParser);
var pMap = ReadPeakMap(option.PeakFile, option.PeakParser);
var mgfFormat = new MascotGenericFormatWriter <Peak>();
foreach (var key in pMap.Keys)
{
if (hMap.ContainsKey(key))
{
pMap[key].PrecursorMZ = hMap[key].PrecursorMZ;
pMap[key].PrecursorCharge = hMap[key].PrecursorCharge;
}
}
var result = pMap.Values.ToList();
//foreach (var key in hMap.Keys)
//{
// if (!pMap.ContainsKey(key))
// {
// result.Add(pMap[key]);
// }
//}
foreach (var v in result)
{
v.Annotations.Remove(MascotGenericFormatConstants.TITLE_TAG);
}
result.Sort((m1, m2) => m1.FirstScan - m2.FirstScan);
option.Writer.WriteToFile(targetFile, result);
return(new string[] { targetFile });
}
public override IEnumerable <string> Process(string fileName)
{
var result = new FileInfo(targetDir + "\\" + Path.ChangeExtension(new FileInfo(fileName).Name, ".mgf")).FullName;
int charge = 1;
PeakList <Peak> ms1 = new PeakList <Peak>();
//读取ms1
List <string> comments = new List <string>();
comments.Add("COM=" + software);
using (StreamReader sr = new StreamReader(fileName))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("COM="))
{
comments.Add(line);
continue;
}
if (line.StartsWith("BEGIN IONS"))
{
break;
}
comments.Add(line);
var parts = line.Split('\t');
if (parts.Length == 2)
{
try
{
ms1.Add(new Peak(double.Parse(parts[0]), double.Parse(parts[1])));
}
catch (Exception) { }
}
}
}
MascotGenericFormatReader <Peak> reader = new MascotGenericFormatReader <Peak>();
var pkls = reader.ReadFromFile(fileName);
foreach (var pkl in pkls)
{
var mzTolerance = PrecursorUtils.ppm2mz(pkl.PrecursorMZ, precursorTolerance);
var peak = ms1.FindPeak(pkl.PrecursorMZ, mzTolerance).FindMaxIntensityPeak();
if (peak == null)
{
pkl.PrecursorIntensity = ms1.Min(m => m.Intensity);
}
else
{
pkl.PrecursorIntensity = peak.Intensity;
}
}
pkls.Sort((m1, m2) => m2.PrecursorIntensity.CompareTo(m1.PrecursorIntensity));
for (int i = 0; i < pkls.Count; i++)
{
var line = pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] as string;
var m = reg.Match(line);
string experimental;
if (m.Success)
{
experimental = m.Groups[1].Value;
var m2 = nameReg.Match(experimental);
if (m2.Success)
{
if (m2.Groups[2].Value.Length == 1)
{
experimental = m2.Groups[1].Value + "0" + m2.Groups[2].Value;
}
}
}
else
{
experimental = pkls[i].Experimental;
}
pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] = string.Format("{0}.{1}.{2:0}.{3}.dta", experimental, i + 1, pkls[i].PrecursorIntensity, charge);
}
var writer = new MascotGenericFormatWriter <Peak>();
writer.Comments.AddRange(comments);
writer.WriteToFile(result, pkls);
return(new string[] { result });
}
