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;
 }
Beispiel #6
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        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();
        }
Beispiel #7
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 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)
 {
 }
Beispiel #8
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 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)
 {
 }
Beispiel #9
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 public StaticMod(string name, string aas, ModTerminus? term, LabelAtoms labelAtoms)
     : this(name, aas, term, null, labelAtoms, null, null)
 {
 }
Beispiel #10
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 public StaticMod(string name, string aas, ModTerminus? term, string formula)
     : this(name, aas, term, formula, LabelAtoms.None, null, null)
 {
 }