public ModifiedPeptide SetVariableModifications(PeptideModificationState varMods, int index)
{
ModifiedPeptide result = CreateNonmodifiedVersion(index);
result.modifications = varMods;
if (varMods != null)
{
result.mass += varMods.GetDeltaMass();
}
return(result);
}
public static ModifiedPeptide Read(BinaryReader reader)
{
try {
ModifiedPeptide result = new ModifiedPeptide();
result.peptideIndex = reader.ReadInt32();
result.modifications = PeptideModificationState.Read(reader);
result.mass = reader.ReadDouble();
return(result);
} catch (EndOfStreamException) {
return(null);
}
}
public static double ApplyFixedModifications(Modification[] mods, string sequence, bool isNterm, bool isCterm, int len,
out PeptideModificationCounts modCounts)
{
ushort[] modifications = new ushort[len];
for (int i = 0; i < len; i++)
{
modifications[i] = ushort.MaxValue;
}
ushort nTermModification = ushort.MaxValue;
ushort cTermModification = ushort.MaxValue;
double deltaMass = 0;
foreach (Modification mod in mods)
{
deltaMass += ApplyFixedModification(mod, sequence, isNterm, isCterm, modifications,
ref nTermModification, ref cTermModification);
}
modCounts = PeptideModificationState.ProjectToCounts(modifications, nTermModification, cTermModification);
return(deltaMass);
}
public PeptideModificationState[] ApplyVariableModificationsFixedNumbers(Modification[] modifications, int[] counts,
out bool incomplete)
{
incomplete = false;
PeptideModificationState[] mods = new PeptideModificationState[] { CreateNonmodifiedVersion() };
int limit = (int)Math.Round(6000000.0 / sequence.ToString().Length / modifications.Length);
for (int i = 0; i < modifications.Length; i++)
{
bool incompl;
Modification mod = modifications[i];
int n = counts[i];
mods = ApplyVariableModificationFixedNumber(mods, mod, n, out incompl, limit);
if (incompl)
{
incomplete = true;
}
}
return(mods);
}
public static Peptide Read(BinaryReader reader)
{
Peptide result = new Peptide();
result.sequence = AASequence.Read(reader);
if (result.sequence == null)
{
return(null);
}
result.monoIsotopicMass = reader.ReadDouble();
int nproteins = reader.ReadInt32();
for (int i = 0; i < nproteins; i++)
{
result.proteinIndices.Add(reader.ReadInt32());
result.proteinOffsets.Add(reader.ReadInt32());
result.residueBefore.Add(reader.ReadByte());
result.residueAfter.Add(reader.ReadByte());
}
result.fixedModifications = PeptideModificationState.Read(reader);
return(result);
}
public ModifiedPeptide(DatabasePeptide peptide, int peptideIndex, string sequence)
{
this.peptideIndex = peptideIndex;
modifications = new PeptideModificationState(sequence.Length);
mass = peptide.GetMonoIsotopicMass(sequence);
}
public ModifiedPeptide(Peptide peptide, int peptideIndex)
{
this.peptideIndex = peptideIndex;
modifications = new PeptideModificationState(peptide.Sequence.Length);
mass = peptide.MonoIsotopicMass;
}
public Peptide(string sequence)
{
this.sequence = new AASequence(sequence);
monoIsotopicMass = MonoIsotopicMass;
fixedModifications = new PeptideModificationState(sequence.Length);
}
private PeptideModificationState[] ApplyVariableModificationFixedNumber(PeptideModificationState peptide,
Modification mod, int n,
out bool incomplete)
{
incomplete = false;
if (n == 0)
{
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.anyNterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.anyCterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.proteinNterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
if (mod.GetPosition() == ModificationPosition.proteinCterm)
{
if (n > 1)
{
return(new PeptideModificationState[0]);
}
if (peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
return(new PeptideModificationState[] { q });
}
return(new PeptideModificationState[0]);
}
string s = Sequence;
switch (mod.GetTermType(0))
{
case ModificationSiteType.aa: {
HashSet <int> ind = new HashSet <int>();
for (int j = 0; j < s.Length; j++)
{
for (int i = 0; i < mod.AaCount; i++)
{
if (s[j] == mod.GetAaAt(i) && peptide.GetModificationAt(j) == ushort.MaxValue)
{
ind.Add(j);
}
}
}
int[] indices = ind.ToArray();
if (indices.Length < n)
{
return(new PeptideModificationState[0]);
}
List <PeptideModificationState> result = new List <PeptideModificationState>();
bool incompl;
int[][] comb = NumUtil.GetCombinations(indices.Length, n, 10000, out incompl);
if (incompl)
{
incomplete = incompl;
}
for (int j = 0; j < comb.Length; j++)
{
int[] iind = ArrayUtil.SubArray(indices, comb[j]);
PeptideModificationState q = peptide.Clone();
for (int k = 0; k < iind.Length; k++)
{
q.SetModificationAt(iind[k], mod.Index);
}
result.Add(q);
}
return(result.ToArray());
}
case ModificationSiteType.nterm: {
if (n > 1)
{
return(new PeptideModificationState[0]);
}
for (int i = 0; i < mod.AaCount; i++)
{
List <PeptideModificationState> toBeAdded = new List <PeptideModificationState>();
if (s[0] == mod.GetAaAt(i) && peptide.GetNTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetNTermModification(mod.Index);
toBeAdded.Add(q);
}
if (toBeAdded.Count > 0)
{
return(toBeAdded.ToArray());
}
}
return(new PeptideModificationState[0]);
}
case ModificationSiteType.cterm: {
if (n > 1)
{
return(new PeptideModificationState[0]);
}
for (int i = 0; i < mod.AaCount; i++)
{
List <PeptideModificationState> toBeAdded = new List <PeptideModificationState>();
if (s[s.Length - 1] == mod.GetAaAt(i) && peptide.GetCTermModification() == ushort.MaxValue)
{
PeptideModificationState q = peptide.Clone();
q.SetCTermModification(mod.Index);
toBeAdded.Add(q);
}
if (toBeAdded.Count > 0)
{
return(toBeAdded.ToArray());
}
}
return(new PeptideModificationState[0]);
}
}
throw new Exception("Never get here.");
}