public static StaticMod GetStaticMod(int uniModId, char aa, ModTerminus? modTerminus)
{
// Always check the simple AA mod case
var idKeysToTry = new List<UniMod.UniModIdKey>
{
new UniMod.UniModIdKey
{
Id = uniModId,
Aa = aa,
AllAas = false,
Terminus = null
},
new UniMod.UniModIdKey
{
Id = uniModId,
Aa = aa,
AllAas = true,
Terminus = null
}
};
// If mod is on a terminal AA, it could still be a non-terminal mod
// Or a terminal mod that applies to any amino acid
if (modTerminus != null)
{
idKeysToTry.Add(new UniMod.UniModIdKey
{
Id = uniModId,
Aa = aa,
AllAas = false,
Terminus = modTerminus
});
idKeysToTry.Add(new UniMod.UniModIdKey
{
Id = uniModId,
Aa = aa,
AllAas = true,
Terminus = modTerminus
});
}
foreach (var key in idKeysToTry)
{
StaticMod staticMod;
if (UniMod.DictUniModIds.TryGetValue(key, out staticMod))
return staticMod;
}
return null;
}
public AATermKey(byte? aa, ModTerminus? terminus)
{
_aa = aa;
_terminus = terminus;
}
private bool? IsAAConflict(byte? aa, ModTerminus? terminus)
{
return _aasConflictingMods[GetAAConflictIndex(aa, terminus)];
}
private void AddConflictKey(byte? aa, ModTerminus? terminus, bool startingValue)
{
int i = GetAAConflictIndex(aa, terminus);
_aasConflictingMods[i] = startingValue || _aasConflictingMods[i].HasValue;
}
private static int GetAAConflictIndex(byte? aa, ModTerminus? terminus)
{
int i = 0;
if (terminus.HasValue)
i = ((int)terminus + 1)*30;
return aa.HasValue
? aa.Value - i
: i;
}
public StaticMod(string name,
string aas,
ModTerminus? term,
bool isVariable,
string formula,
LabelAtoms labelAtoms,
RelativeRT relativeRT,
double? monoMass,
double? avgMass,
IList<FragmentLoss> losses,
int? uniModId,
string shortName)
: base(name)
{
AAs = aas;
Terminus = term;
IsVariable = IsExplicit = isVariable; // All variable mods are explicit
Formula = formula;
LabelAtoms = labelAtoms;
RelativeRT = relativeRT;
MonoisotopicMass = monoMass;
AverageMass = avgMass;
Losses = losses;
UnimodId = uniModId;
ShortName = shortName;
Validate();
}
public StaticMod(string name, string aas, ModTerminus? term, bool isVariable, string formula,
LabelAtoms labelAtoms, RelativeRT relativeRT, double? monoMass, double? avgMass, IList<FragmentLoss> losses)
: this(name, aas, term, isVariable, formula, labelAtoms, relativeRT, monoMass, avgMass, losses, null, null)
{
}
public StaticMod(string name, string aas, ModTerminus? term,
string formula, LabelAtoms labelAtoms, double? monoMass, double? avgMass)
: this(name, aas, term, false, formula, labelAtoms, RelativeRT.Matching, monoMass, avgMass, null, null, null)
{
}
public StaticMod(string name, string aas, ModTerminus? term, LabelAtoms labelAtoms)
: this(name, aas, term, null, labelAtoms, null, null)
{
}
public StaticMod(string name, string aas, ModTerminus? term, string formula)
: this(name, aas, term, formula, LabelAtoms.None, null, null)
{
}