public SearchModification(Modification mod, char targetResidue, SequenceLocation loc, bool isFixedModification)
{
Modification = mod;
TargetResidue = targetResidue;
Location = loc;
IsFixedModification = isFixedModification;
}
/// <summary>
/// Storing all possible combinations of modifications up to MaxNumDynModsPerSequence
/// </summary>
/// <param name="modifications">array of modifications</param>
/// <param name="maxNumDynModsPerSequence">number of maximum modifications</param>
public ModificationParams(Modification[] modifications, int maxNumDynModsPerSequence)
{
_modifications = modifications;
_maxNumDynModsPerSequence = maxNumDynModsPerSequence;
CataloguePossibleModificationCombinations();
GenerateModCombMap();
}
// Generate an amino acid map with Cys static modification
public AminoAcidSet(Modification cysMod): this()
{
foreach (var loc in AllSequenceLocations)
{
var residueMap = _locationSpecificResidueMap[loc];
residueMap['C'] = new ModifiedAminoAcid(residueMap['C'], cysMod);
}
}
public ModifiedAminoAcid(AminoAcid aa, Modification modification)
: base(aa.Residue, aa.Name+"+"+modification.Name, aa.Composition+modification.Composition)
{
var modAa = aa as ModifiedAminoAcid;
if(modAa == null) _modification = modification; // aa is not modified
else // aa is already modified
{
_modification = Modification.RegisterAndGetModification(modAa.Modification.Name+"+"+modification.Name, Composition);
}
}
public static void Register(Modification modification)
{
NameToModMap.Add(modification.Name, modification);
var massStr = string.Format("{0:N3}", modification.Composition.Mass);
IList<Modification> modList;
if (!MassToModMap.TryGetValue(massStr, out modList))
{
modList = new List<Modification> { modification };
MassToModMap[massStr] = modList;
}
modList.Add(modification);
}
// Added by Chris
/// <summary>
/// Unregister a modification by name.
/// Added by Chris.
/// </summary>
/// <param name="modification">The modification to remove.</param>
public static void UnregisterModification(Modification modification)
{
if (NameToModMap.ContainsKey(modification.Name)) NameToModMap.Remove(modification.Name);
var massStr = string.Format("{0:N3}", modification.Mass);
if (MassToModMap.ContainsKey(massStr)) MassToModMap.Remove(massStr);
}
// Added by Chris
/// <summary>
/// Register a new modification or update an existing modification.
/// </summary>
/// <param name="name">The name of the modification.</param>
/// <param name="mass">The mass of the modification.</param>
/// <returns>Registered modification.</returns>
public static Modification UpdateAndGetModification(string name, double mass)
{
if (NameToModMap.ContainsKey(name)) NameToModMap.Remove(name);
var massStr = string.Format("{0:N3}", mass);
if (MassToModMap.ContainsKey(massStr)) MassToModMap.Remove(massStr);
var modification = new Modification(-1, mass, name);
Register(modification);
return modification;
}
public static Modification RegisterAndGetModification(string name, double mass)
{
var modList = GetFromMass(mass);
if (modList != null && modList.Any()) return modList[0];
var mod = Get(name);
if (mod != null) return mod;
mod = new Modification(-1, mass, name);
Register(mod);
return mod;
}
public static Modification RegisterAndGetModification(string name, Composition.Composition composition)
{
var mod = Get(name);
if (mod != null) return mod;
mod = new Modification(-1, composition, name);
Register(mod);
return mod;
}
