/// <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));
}
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));
}
}
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));
}
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))));
}
protected bool Equals(PeptideLibraryKey other)
{
return(string.Equals(ModifiedSequence, other.ModifiedSequence) &&
Charge == other.Charge);
}
