public override void Open(string fileName)
{
Close();
sr = new StreamReader(fileName);
this.FileName = fileName;
iter = new MascotGenericFormatIterator <Peak>(sr);
string line;
int scan = 1;
long position = 0;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(MascotGenericFormatConstants.MSMS_SCAN_TAG))
{
Match m = scanRegex.Match(line);
scan = Convert.ToInt32(m.Groups[1].Value);
positions[scan] = new PositionClass()
{
Position = position
};
}
else if (line.StartsWith(MascotGenericFormatConstants.RETENTION_TIME_TAG))
{
positions[scan].RetentionTimeInSecond = MyConvert.ToDouble(line.Substring(MascotGenericFormatConstants.RETENTION_TIME_TAG.Length + 1));
}
else if (line.StartsWith(MascotGenericFormatConstants.END_PEAK_LIST_TAG))
{
position = StreamUtils.GetCharpos(sr);
}
}
List <int> scans = new List <int>(positions.Keys);
if (scans.Count > 0)
{
firstScan = scans[0];
lastScan = scans[scans.Count - 1];
}
else
{
firstScan = 0;
lastScan = -1;
}
}
public void Test()
{
using (var sr = new StreamReader(TestContext.CurrentContext.TestDirectory + "/../../../data//Ribo B 645.txt"))
{
var iter = new MascotGenericFormatIterator <Peak>(sr);
PeakList <Peak> expPkl = iter.Next();
var score = new XCorrelationSpectrumScore <Peak>(expPkl);
var builder = new ETDPeptideCSeriesBuilder <IonTypePeak>(2000, 3);
builder.CurAminoacids['*'].ResetMass(1217.117, 1217.117);
List <IonTypePeak> thePkl = builder.Build("SRN*LTK");
double Score = score.Calculate(thePkl);
Console.Out.WriteLine("Score={0:0.0000}", Score);
}
}
public void Test()
{
using (var sr = new StreamReader("../../../data/Ribo B 645.txt"))
{
var iter = new MascotGenericFormatIterator<Peak>(sr);
PeakList<Peak> expPkl = iter.Next();
var score = new XCorrelationSpectrumScore<Peak>(expPkl);
var builder = new ETDPeptideCSeriesBuilder<IonTypePeak>(2000, 3);
builder.CurAminoacids['*'].ResetMass(1217.117, 1217.117);
List<IonTypePeak> thePkl = builder.Build("SRN*LTK");
double Score = score.Calculate(thePkl);
Console.Out.WriteLine("Score={0:0.0000}", Score);
}
}
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 mgfFilename)
{
String mgfName = Path.GetFileNameWithoutExtension(mgfFilename);
using (var sw = new StreamWriter(targetFile))
{
sw.WriteLine("H\tCreationDate\t{0:yyyyMMdd}", DateTime.Now);
sw.WriteLine("H\tExtractor\tProteomicsTools");
using (var sr = new StreamReader(mgfFilename))
{
bool bProcessing = sr.BaseStream.Length > 0;
var reader = new MascotGenericFormatIterator <Peak>(sr);
this.scanIndex = 0;
if (bProcessing)
{
Progress.SetMessage("Converting " + mgfFilename + " ...");
Progress.SetRange(0, sr.BaseStream.Length);
}
Progress.SetPosition(0);
while (reader.HasNext())
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = reader.Next();
if (bProcessing)
{
Progress.SetPosition(sr.BaseStream.Position);
}
int[] charges;
if (0 != pkl.PrecursorCharge)
{
charges = new[] { pkl.PrecursorCharge };
}
else if (IsWiff(pkl))
{
charges = new[] { 1 };
}
else
{
charges = new[] { 2, 3 };
}
var sf = GetFilename(pkl, mgfName);
sw.WriteLine("S\t{0}\t{1}\t{2}", sf.FirstScan, sf.LastScan, pkl.PrecursorMZ);
foreach (var charge in charges)
{
sw.WriteLine("Z\t{0}\t{1:0.#####}", charge, PrecursorUtils.MzToMH(pkl.PrecursorMZ, charge, true));
}
foreach (var peak in pkl)
{
sw.WriteLine("{0:0.#####}\t{1:0.#}", peak.Mz, peak.Intensity);
}
}
Progress.SetMessage("Converting " + mgfFilename + " finished.");
}
}
return(new[] { this.targetFile });
}
