public static Modification[] GetModifiedVersions(char aa, SilacType type, SilacLabel[] labels1, SilacLabel[] labels2)
{
AminoAcid a = AminoAcid.FromLetter(aa);
switch (type)
{
case SilacType.Singlets:
return(new Modification[1]);
case SilacType.Doublets:
Modification[] result = new Modification[2];
if (a.HasFittingLabel(labels1))
{
SilacLabel sl = a.GetFittingLabel(labels1);
result[1] = Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(sl)];
}
return(result);
case SilacType.Triplets:
result = new Modification[3];
if (a.HasFittingLabel(labels1))
{
SilacLabel sl = a.GetFittingLabel(labels1);
result[1] = Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(sl)];
}
if (a.HasFittingLabel(labels2))
{
SilacLabel sl = a.GetFittingLabel(labels2);
result[2] = Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(sl)];
}
return(result);
}
throw new Exception("Never get here.");
}
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");
}
private static int CalcSilacIndex(char aa, PeptideModificationState labelMods, string sequence, SilacType type,
SilacLabel[] labels1, SilacLabel[] labels2)
{
for (int i = 0; i < sequence.Length; i++)
{
if (sequence[i] != aa)
{
continue;
}
ushort m = labelMods.GetModificationAt(i);
if (type == SilacType.Doublets)
{
if (m != ushort.MaxValue)
{
return(1);
}
return(0);
}
if (type == SilacType.Triplets)
{
int ind1 = -1;
for (int j = 0; j < labels1.Length; j++)
{
if (AminoAcid.GetAminoAcidFromLabel(labels1[j]).Letter == aa)
{
ind1 = j;
}
}
int ind2 = -1;
for (int j = 0; j < labels2.Length; j++)
{
if (AminoAcid.GetAminoAcidFromLabel(labels2[j]).Letter == aa)
{
ind2 = j;
}
}
if (ind1 == -1 && ind2 == -1)
{
return(-1);
}
if (ind1 == -1)
{
if (m != ushort.MaxValue)
{
return(2);
}
return(-1);
}
if (ind2 == -1)
{
if (m != ushort.MaxValue)
{
return(1);
}
return(-1);
}
SilacLabel l1 = labels1[ind1];
SilacLabel l2 = labels2[ind2];
if (l1 == l2)
{
if (m == ushort.MaxValue)
{
return(0);
}
return(-1);
}
if (m == ushort.MaxValue)
{
return(0);
}
if (Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(l1)].Index == m)
{
return(1);
}
if (Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(l2)].Index == m)
{
return(2);
}
throw new Exception("Never get here.");
}
throw new Exception("Should never happen.");
}
return(-1);
}
