public Sequence GetSequence(string sequence)
{
Sequence seq;
if (_format == DataFileFormat.Mgf)
{
var sequenceReader = new MgfSequenceReader();
seq = sequenceReader.GetSequence(sequence);
}
else
{
seq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequence);
}
return seq;
}
public Sequence GetSequence(string sequence)
{
Sequence seq;
if (_format == DataFileFormat.Mgf)
{
var sequenceReader = new MgfSequenceReader();
seq = sequenceReader.GetSequence(sequence);
}
else
{
seq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequence);
}
return(seq);
}
public IList<SpectrumMatch> Read()
{
var specMatches = new List<SpectrumMatch>();
var file = File.ReadLines(_fileName);
var mgfState = MgfState.Label;
var sequence = "";
int scanNum = 0, charge = 0;
var peaks = new List<Peak>();
var peptideSet = new HashSet<string>();
foreach (var line in file)
{
switch (mgfState)
{
case MgfState.Label:
if (line == "BEGIN IONS") mgfState = MgfState.Parameter;
else throw new FormatException("Invalid MGF file.");
break;
case MgfState.Parameter:
var parameter = line.Split('=');
if (parameter.Length < 2) throw new FormatException("Invalid line in MGF file: " + line);
if (parameter[0] == "SEQ") sequence = parameter[1];
else if (parameter[0] == "SCANS") scanNum = Convert.ToInt32(parameter[1]);
else if (parameter[0] == "CHARGE")
{
var chargeStr = parameter[1].Substring(0, parameter[1].Length - 1);
charge = Convert.ToInt32(chargeStr);
mgfState = MgfState.Peak;
if (sequence == "" || scanNum == 0 || charge == 0)
throw new FormatException("Incomplete spectrum entry.");
}
break;
case MgfState.Peak:
if (line == "END IONS")
{
if (peaks.Count == 0) throw new FormatException("Empty peak list.");
mgfState = MgfState.Label;
if (peptideSet.Contains(sequence))
{
sequence = "";
scanNum = 0;
charge = 0;
peaks.Clear();
continue;
}
peptideSet.Add(sequence);
var spectrum = new ProductSpectrum(peaks, scanNum) { MsLevel = 2 };
var sequenceReader = new MgfSequenceReader();
var seq = sequenceReader.GetSequence(sequence);
var specMatch = new SpectrumMatch(seq, spectrum, scanNum, charge, _decoy);
sequence = "";
scanNum = 0;
charge = 0;
specMatches.Add(specMatch);
peaks.Clear();
}
else
{
var parts = line.Split('\t');
if (parts.Length < 2) throw new FormatException("Invalid line in MGF file: " + line);
var mz = Convert.ToDouble(parts[0]);
var intensity = Convert.ToDouble(parts[1]);
peaks.Add(new Peak(mz, intensity));
}
break;
}
}
return specMatches;
}
