public override bool Equals(object anObject)
{
if (this == anObject)
{
return(true);
}
if (anObject is PeptideModificationState)
{
PeptideModificationState other = (PeptideModificationState)anObject;
if (other.NTermModification != NTermModification)
{
return(false);
}
if (other.CTermModification != CTermModification)
{
return(false);
}
if (other.Length != Length)
{
return(false);
}
for (int i = 0; i < Length; i++)
{
if (other.GetModificationAt(i) != GetModificationAt(i))
{
return(false);
}
}
return(true);
}
return(false);
}
public PeptideModificationState GetTrueModifications()
{
PeptideModificationState result = GetFreshCopy(Length);
if (NTermModification != ushort.MaxValue && Modification.IsStandardVarMod(NTermModification))
{
result.NTermModification = NTermModification;
}
if (CTermModification != ushort.MaxValue && Modification.IsStandardVarMod(CTermModification))
{
result.CTermModification = CTermModification;
}
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m == ushort.MaxValue || !Modification.IsStandardVarMod(m))
{
result.SetModificationAt(i, ushort.MaxValue);
}
else
{
result.SetModificationAt(i, GetModificationAt(i));
}
}
return(result);
}
public PeptideModificationState GetLabelModifications(ushort[] labelMods, string sequence)
{
PeptideModificationState result = GetFreshCopy(Length);
if (NTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(NTermModification))
{
result.NTermModification = NTermModification;
}
if (CTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(CTermModification))
{
result.CTermModification = CTermModification;
}
for (int i = 0; i < Length; i++)
{
ushort m = GetModificationAt(i);
if (m != ushort.MaxValue && !Modification.IsStandardVarMod(m))
{
result.SetModificationAt(i, m);
}
else
{
result.SetModificationAt(i, ushort.MaxValue);
}
}
foreach (ushort labelMod in labelMods)
{
if (!Modification.IsStandardVarMod(labelMod))
{
Modification mod = Tables.ModificationList[labelMod];
if (mod.IsInternal)
{
for (int j = 0; j < mod.AaCount; j++)
{
char c = mod.GetAaAt(j);
for (int i = 0; i < Length; i++)
{
if (sequence[i] == c)
{
result.SetModificationAt(i, mod.Index);
}
}
}
}
else
{
if (mod.IsNterminal)
{
result.NTermModification = mod.Index;
}
else
{
result.CTermModification = mod.Index;
}
}
}
}
return(result);
}
public PeptideModificationState Revert()
{
PeptideModificationState result = Clone();
for (int i = 1; i < Modifications.Length - 1; i++)
{
result.Modifications[i] = Modifications[Modifications.Length - 1 - i];
}
result.Modifications[Modifications.Length - 1] = Modifications[Modifications.Length - 1];
result.Modifications[0] = Modifications[0];
return(result);
}
FillFixedModifications(string sequence, IDictionary <char, ushort> fmods)
{
PeptideModificationState result = new PeptideModificationState(sequence.Length);
for (int i = 0; i < sequence.Length; i++)
{
if (fmods.ContainsKey(sequence[i]))
{
result.Modifications[i] = fmods[sequence[i]];
}
}
return(result);
}
public PeptideModificationState GetFreshCopy(int len)
{
PeptideModificationState result = new PeptideModificationState {
NTermModification = ushort.MaxValue,
CTermModification = ushort.MaxValue,
Modifications = new ushort[len]
};
for (int i = 0; i < len; i++)
{
result.Modifications[i] = ushort.MaxValue;
}
return(result);
}
public static PeptideModificationState Read(BinaryReader reader)
{
PeptideModificationState result = new PeptideModificationState {
CTermModification = reader.ReadUInt16(), NTermModification = reader.ReadUInt16()
};
int len = reader.ReadInt32();
result.Modifications = new ushort[len];
for (int i = 0; i < result.Modifications.Length; i++)
{
result.Modifications[i] = reader.ReadUInt16();
}
return(result);
}
private static (string, PeptideModificationState) FromString(string nt, string ct, string[] q)
{
PeptideModificationState result = new PeptideModificationState(q.Length);
(char _, ushort mod) = GetAaAndMod(nt);
result.NTermModification = mod;
(_, mod) = GetAaAndMod(ct);
result.CTermModification = mod;
char[] sequence = new char[q.Length];
for (int i = 0; i < q.Length; i++)
{
(sequence[i], result.Modifications[i]) = GetAaAndMod(ct);
}
return(new string(sequence), result);
}
public PeptideModificationState RemoveLabelModifications()
{
PeptideModificationState result = Clone();
if (NTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(NTermModification))
{
result.NTermModification = ushort.MaxValue;
}
if (CTermModification != ushort.MaxValue && !Modification.IsStandardVarMod(CTermModification))
{
result.CTermModification = ushort.MaxValue;
}
for (int i = 0; i < Modifications.Length; i++)
{
if (Modifications[i] != ushort.MaxValue && !Modification.IsStandardVarMod(Modifications[i]))
{
result.Modifications[i] = ushort.MaxValue;
}
}
return(result);
}
public PeptideModificationState RemoveNonCompositionMods()
{
PeptideModificationState result = Clone();
const ushort m = ushort.MaxValue - 10;
if (result.NTermModification >= m)
{
result.NTermModification = ushort.MaxValue;
}
if (result.CTermModification >= m)
{
result.CTermModification = ushort.MaxValue;
}
for (int i = 0; i < Modifications.Length; i++)
{
if (result.Modifications[i] >= m)
{
result.Modifications[i] = ushort.MaxValue;
}
}
return(result);
}
public PeptideModificationState GetFreshCopy(int len)
{
PeptideModificationState result = new PeptideModificationState{
NTermModification = ushort.MaxValue,
CTermModification = ushort.MaxValue,
Modifications = new ushort[len]
};
for (int i = 0; i < len; i++){
result.Modifications[i] = ushort.MaxValue;
}
return result;
}
public static PeptideModificationState Read(BinaryReader reader)
{
PeptideModificationState result = new PeptideModificationState{
CTermModification = reader.ReadUInt16(),
NTermModification = reader.ReadUInt16()
};
int len = reader.ReadInt32();
result.Modifications = new ushort[len];
for (int i = 0; i < result.Modifications.Length; i++){
result.Modifications[i] = reader.ReadUInt16();
}
return result;
}
public static PeptideModificationState FillFixedModifications(string sequence, IDictionary<char, ushort> fmods)
{
PeptideModificationState result = new PeptideModificationState(sequence.Length);
for (int i = 0; i < sequence.Length; i++){
if (fmods.ContainsKey(sequence[i])){
result.Modifications[i] = fmods[sequence[i]];
}
}
return result;
}
