Exemplo n.º 1
0
        /// <summary>
        /// Given two keys that match each other (i.e. the modification masses are within the other's margin of error)
        /// return a key which has the lower precision of the two.
        /// For instance, if one key is C[+57.021464]PEPTIDER[+10] and the is C[+57.02]PEPTIDEK[10.0083],
        /// the result be C[+57.02]PEPTIDER[+10].
        /// </summary>
        private PeptideLibraryKey MostGeneralPeptideKey(PeptideLibraryKey key1, PeptideLibraryKey key2)
        {
            Assume.AreEqual(key1.UnmodifiedSequence, key2.UnmodifiedSequence);
            var mods1 = key1.GetModifications();
            var mods2 = key2.GetModifications();

            Assume.AreEqual(mods1.Count, mods2.Count);
            var newMods = new List <KeyValuePair <int, string> >(mods1.Count);

            for (int i = 0; i < mods1.Count; i++)
            {
                var mod1 = mods1[i];
                var mod2 = mods2[i];
                Assume.AreEqual(mod1.Key, mod2.Key);
                if (mod1.Value == mod2.Value)
                {
                    newMods.Add(mod1);
                    continue;
                }
                MassModification massMod1 = MassModification.Parse(mod1.Value);
                MassModification massMod2 = MassModification.Parse(mod2.Value);
                if (massMod1.Precision <= massMod2.Precision)
                {
                    newMods.Add(mod1);
                }
                else
                {
                    newMods.Add(mod2);
                }
            }
            return(new PeptideLibraryKey(MakeModifiedSequence(key1.UnmodifiedSequence, newMods), key1.Charge));
        }
Exemplo n.º 2
0
                public Peptide(PeptideLibraryKey peptideLibraryKey) : this((LibraryKey)peptideLibraryKey)
                {
                    var modifications = peptideLibraryKey.GetModifications();

                    if (modifications.Count > 0)
                    {
                        ModificationIndexes = ImmutableList.ValueOf(modifications.Select(mod => mod.Key));
                        ModificationNames   = ImmutableList.ValueOf(modifications.Select(mod => mod.Value));
                    }
                }
Exemplo n.º 3
0
        public override LibraryKey ValueFromCache(ValueCache valueCache)
        {
            var libraryKey = this;

            if (valueCache.TryGetCachedValue(ref libraryKey))
            {
                return(libraryKey);
            }
            libraryKey = new PeptideLibraryKey
            {
                ModifiedSequence   = valueCache.CacheValue(ModifiedSequence),
                UnmodifiedSequence = valueCache.CacheValue(UnmodifiedSequence),
                Charge             = Charge,
            };
            return(valueCache.CacheValue(libraryKey));
        }
Exemplo n.º 4
0
 private IEnumerable <PeptideLibraryKey> MergePeptideLibraryKey(ICollection <PeptideLibraryKey> thisKeys, PeptideLibraryKey thatKey)
 {
     while (true)
     {
         PeptideLibraryKey mostGeneralKey = thatKey;
         foreach (var thisKey in thisKeys)
         {
             if (KeysMatch(thisKey, mostGeneralKey))
             {
                 mostGeneralKey = MostGeneralPeptideKey(thisKey, mostGeneralKey);
             }
         }
         if (Equals(mostGeneralKey, thatKey))
         {
             break;
         }
         thatKey = mostGeneralKey;
     }
     return(new[] { thatKey }.Concat(thisKeys.Where(key => !KeysMatch(thatKey, key))));
 }
Exemplo n.º 5
0
 protected bool Equals(PeptideLibraryKey other)
 {
     return(string.Equals(ModifiedSequence, other.ModifiedSequence) &&
            Charge == other.Charge);
 }