public static void WriteSearchEngineParams(SearchEngineParams msh, string[] silacMsmNames, string isoMsmName,
string peakMsmName,
SilacLabel[][] l, SilacLabel[] allLabels, bool labelModsForNonSilac)
{
WriteSearchEngineParams(peakMsmName, allLabels, labelModsForNonSilac, true, (SearchEngineParams)msh.Clone(), " - " + ".peak.msm");
WriteSearchEngineParams(isoMsmName, allLabels, labelModsForNonSilac, true, (SearchEngineParams)msh.Clone(), " - " + ".peak.msm");
for (int i = 0; i < silacMsmNames.GetLength(0); i++)
{
WriteSearchEngineParams(silacMsmNames[i], l[i], true, false, (SearchEngineParams)msh.Clone(), " - " + ".sil" + i + ".msm");
}
}
public static void WriteSearchEngineParams(string msmName, SilacLabel[] labels, bool addLabels, bool variableMods,
SearchEngineParams msh, string titleSuffix)
{
if (addLabels)
{
for (int i = 0; i < labels.Length; i++)
{
if (variableMods)
{
msh.AddVariabeModification(AminoAcid.GetMascotModificationStringForLabel(labels[i]));
}
else
{
msh.AddFixedModification(AminoAcid.GetMascotModificationStringForLabel(labels[i]));
}
}
}
msh.Title += titleSuffix;
msh.Write(msmName.Substring(0, msmName.Length - 4) + ".par");
}