public static void ParseMsm(string msmName, string[] silacMsmNames, string isoMsmName, string peakMsmName,
string polyMsmName, IPeakList peakList, out int silacCount, out int isoCount,
out int peakCount,
out int polyCount, SilacType silacType, double isotopeCorrelationThreshold)
{
HashSet <int> scanNumbers = new HashSet <int>();
StreamReader reader = new StreamReader(msmName);
StreamWriter[] silacWriters = new StreamWriter[silacMsmNames.GetLength(0)];
for (int i = 0; i < silacWriters.GetLength(0); i++)
{
silacWriters[i] = new StreamWriter(silacMsmNames[i]);
}
StreamWriter isoWriter = new StreamWriter(isoMsmName);
StreamWriter peakWriter = new StreamWriter(peakMsmName);
StreamWriter polyWriter = new StreamWriter(polyMsmName);
string line;
List <string> buffer = new List <string>();
string title = null;
string mass = null;
silacCount = 0;
isoCount = 0;
peakCount = 0;
polyCount = 0;
while ((line = reader.ReadLine()) != null)
{
if (line.IndexOf("BEGIN IONS") != -1)
{
buffer = new List <string>();
}
else if (line.IndexOf("PEPMASS") != -1)
{
mass = line;
}
else if (line.IndexOf("CHARGE") != -1)
{
}
else if (line.IndexOf("TITLE") != -1)
{
title = line;
}
else if (line.IndexOf("END IONS") != -1)
{
ProcessMsm(buffer.ToArray(), title, mass, scanNumbers, silacWriters, isoWriter, peakWriter, polyWriter,
peakList, isotopeCorrelationThreshold, silacType,
ref silacCount, ref isoCount, ref peakCount, ref polyCount);
}
else
{
if (line.Length > 0)
{
buffer.Add(line);
}
}
}
reader.Close();
for (int i = 0; i < silacWriters.GetLength(0); i++)
{
silacWriters[i].Close();
}
isoWriter.Close();
peakWriter.Close();
polyWriter.Close();
}
