public bool IsMatch(string sequence, IonType ionType, int cleavageOffset)
{
if (!IsFragment)
{
return(false);
}
int ordinal = Transition.OffsetToOrdinal(ionType, cleavageOffset, sequence.Length);
if (ordinal < MinFragmentLength)
{
return(false);
}
char aaN = Transition.GetFragmentNTermAA(sequence, cleavageOffset);
char aaC = Transition.GetFragmentCTermAA(sequence, cleavageOffset);
// Make sure the specified amino acid is in the fragment set for this ion
char aa = (IsNTerm() ? aaN : aaC);
if (Fragment.IndexOf(aa) == -1)
{
return(false);
}
// Make suer the adjacent amino acid is not in the restricted set for this ion
aa = (IsNTerm() ? aaC : aaN);
if (Restrict != null && Restrict.IndexOf(aa) != -1)
{
return(false);
}
return(true);
}
public bool IsMatch(Target target, IonType ionType, int cleavageOffset)
{
if (!IsFragment)
{
return(false);
}
if (!target.IsProteomic)
{
return(false); // TODO(bspratt) small molecule equivalent?
}
var sequence = target.Sequence;
int ordinal = Transition.OffsetToOrdinal(ionType, cleavageOffset, sequence.Length);
if (ordinal < MinFragmentLength)
{
return(false);
}
char aaN = Transition.GetFragmentNTermAA(sequence, cleavageOffset);
char aaC = Transition.GetFragmentCTermAA(sequence, cleavageOffset);
// Make sure the specified amino acid is in the fragment set for this ion
char aa = (IsNTerm() ? aaN : aaC);
if (Fragment.IndexOf(aa) == -1)
{
return(false);
}
// Make suer the adjacent amino acid is not in the restricted set for this ion
aa = (IsNTerm() ? aaC : aaN);
if (Restrict != null && Restrict.IndexOf(aa) != -1)
{
return(false);
}
return(true);
}
