/// <summary>
/// Removes the specified mod from all locations on this polymer
/// </summary>
/// <param name="mod">The modification to remove from this polymer</param>
public void ClearModifications(IHasMass mod)
{
for (int i = 0; i <= Length + 1; i++)
{
if (!mod.Equals(_modifications[i]))
{
continue;
}
MonoisotopicMass -= mod.MonoisotopicMass;
_modifications[i] = null;
}
}
/// <summary>
/// Replaces all instances of the old modification with the new modification in this polymer
/// </summary>
/// <param name="oldMod">The modification to remove</param>
/// <param name="newMod">The modification to replace it with</param>
/// <returns>The number of modifications added to this amino acid polymer</returns>
public virtual int ReplaceModification(IHasMass oldMod, IHasMass newMod)
{
if (oldMod == null)
{
throw new MzLibException("Cannot replace a null modification");
}
int count = 0;
for (int i = 0; i < Length + 2; i++)
{
IHasMass mod = GetModification(i);
if (mod == null || !oldMod.Equals(mod))
{
continue;
}
ReplaceMod(i, newMod);
count++;
}
return(count);
}