public bool IsMassMatch(StaticMod mod, double mass)
{
var mod1 = new MassModification(GetDefaultModMass(AA, mod), RoundedTo);
var mod2 = new MassModification(mass, RoundedTo);
if (!mod1.Matches(mod2))
{
return(false);
}
return(IsModMatch(mod));
}
public bool Matches(MassModification that)
{
int minPrecision = Math.Min(Math.Min(Precision, that.Precision), MAX_PRECISION_TO_MATCH);
double thisRound = Math.Round(Mass, minPrecision);
double thatRound = Math.Round(that.Mass, minPrecision);
if (Equals(thisRound, thatRound))
{
return(true);
}
if (Math.Abs(Mass - that.Mass) < .0001)
{
// Anytime two modifications are within .0001 of each other, that is also
// considered good enough since there are search results out there where
// the Cysteine modification differs at that point.
return(true);
}
return(false);
}
private IEnumerable <AAModInfo> EnumerateSequenceInfos(string seq, bool includeUnmod)
{
string aas = FastaSequence.StripModifications(seq);
bool isSpecificHeavy = FastaSequence.OPEN_MOD.All(paren => aas.Length > seq.Count(c => c == paren));
int indexAA = 0;
int indexAAInSeq = 0;
int i = 0;
while (i < seq.Length)
{
var aa = aas[indexAA];
int indexBracket = i + 1;
if (indexBracket < seq.Length && (FastaSequence.OPEN_MOD.Contains(seq[indexBracket])))
{
char openBracket = seq[indexBracket];
bool isHeavy = openBracket == '{';
char closeBracket = FastaSequence.CLOSE_MOD[FastaSequence.OPEN_MOD.IndexOf(c => c == openBracket)];
int indexStart = indexBracket + 1;
int indexClose = seq.IndexOf(closeBracket, indexBracket);
string mod = seq.Substring(indexStart, indexClose - indexStart);
i = indexClose;
ModTerminus?modTerminus = null;
if (indexAA == 0)
{
modTerminus = ModTerminus.N;
}
if (indexAA == aas.Length - 1)
{
modTerminus = ModTerminus.C;
}
string name = null;
double?mass = null;
int roundedTo = 0;
// If passed in modification in UniMod notation, look up the id and find the name and mass
int uniModId;
if (TryGetIdFromUnimod(mod, out uniModId))
{
var staticMod = GetStaticMod(uniModId, aa, modTerminus);
if (staticMod == null)
{
throw ThrowUnimodException(seq, uniModId, indexAA, indexBracket, indexClose);
}
name = staticMod.Name;
isHeavy = !UniMod.IsStructuralModification(name);
// CONSIDER: Mass depends on TransitionPrediction settings for precursors
mass = staticMod.MonoisotopicMass;
roundedTo = DEFAULT_ROUNDING_DIGITS;
}
else
{
MassModification massModification = MassModification.Parse(mod);
if (massModification != null)
{
mass = massModification.Mass;
roundedTo = Math.Min(massModification.Precision, DEFAULT_ROUNDING_DIGITS);
}
else
{
name = mod;
}
}
if (mass.HasValue)
{
mass = Math.Round(mass.Value, roundedTo);
}
var key = new AAModKey
{
Name = name,
Mass = mass,
AA = aa,
Terminus = modTerminus,
UserIndicatedHeavy = isHeavy,
RoundedTo = roundedTo,
AppearsToBeSpecificMod = isSpecificHeavy
};
yield return(new AAModInfo
{
ModKey = key,
IndexAA = indexAA,
IndexAAInSeq = indexAAInSeq,
});
}
else if (includeUnmod)
{
// If need unmodified amino acids (as when
// checking for equality), yield SequenceKeys for these AA's.
var key = new AAModKey
{
AA = aa,
Mass = 0
};
yield return(new AAModInfo
{
ModKey = key,
IndexAA = indexAA,
});
}
// If the next character is a bracket, continue using the same amino
// acid and leave i where it is.
int iNext = i + 1;
if (iNext >= seq.Length || !FastaSequence.OPEN_MOD.Contains(seq[iNext]))
{
i = indexAAInSeq = iNext;
indexAA++;
}
}
}
protected bool Equals(MassModification other)
{
return(Mass.Equals(other.Mass) && Precision == other.Precision);
}
private IEnumerable <AAModInfo> EnumerateSequenceInfos(PeptideLibraryKey peptideLibraryKey, bool allowDuplicates)
{
if (peptideLibraryKey == null)
{
yield break;
}
string sequence = peptideLibraryKey.ModifiedSequence;
bool isSpecificHeavy = !AllAminoAcidsModified(sequence);
char? prevAA = null;
int indexAA = -1;
for (int index = 0; index < sequence.Length; index++)
{
char b = sequence[index];
if (b != '[') // L10N
{
if (isSpecificHeavy)
{
if (index > 0 && prevAA.HasValue)
{
AddConflictKey(prevAA, null, true);
}
if (index == 1)
{
AddConflictKey(prevAA, ModTerminus.N, true);
}
}
prevAA = b;
indexAA++;
}
else
{
ModTerminus?terminus = null;
int startIndex = index + 1;
int endIndex = sequence.IndexOf(']', startIndex);
if (endIndex == -1)
{
endIndex = sequence.Length;
}
if (index == 1)
{
terminus = ModTerminus.N;
}
if (endIndex == sequence.Length - 1)
{
terminus = ModTerminus.C;
}
// Only if prevAA is an amino acid character should AAModInfo be created
// Some libraries, for instance, have been created with the sequence starting
// with a modification before any amino acid, as an attempt at a n-terminal modification
if (prevAA.HasValue && AminoAcid.IsExAA(prevAA.Value))
{
List <string> listMasses;
if (!_dictAAMassPairs.TryGetValue(new AATermKey(prevAA, terminus), out listMasses))
{
listMasses = new List <string>();
_dictAAMassPairs.Add(new AATermKey(prevAA, terminus), listMasses);
}
var modArr = sequence.Substring(startIndex, endIndex - startIndex);
if (allowDuplicates || !listMasses.Contains(modArr))
{
if (!allowDuplicates)
{
listMasses.Add(modArr);
}
string massString = modArr;
var massModification = MassModification.Parse(massString);
if (massModification != null)
{
yield return(new AAModInfo
{
IndexAA = indexAA,
ModKey = new AAModKey
{
AA = prevAA.Value,
Terminus = terminus,
AppearsToBeSpecificMod = isSpecificHeavy,
Mass = massModification.Mass,
RoundedTo = massModification.Precision
}
});
}
// NistLibraryBase writes [?] for any modification it does not understand
else if (!Equals(@"?", massString))
{
// Get more information on a failure that was posted to the exception web page
throw new FormatException(string.Format(Resources.LibKeyModificationMatcher_EnumerateSequenceInfos_The_number___0___is_not_in_the_correct_format_, massString));
}
}
}
prevAA = null;
index = endIndex;
}
}
// If the last AA was not modified, we need to update the conflictingMods array.
if (prevAA.HasValue)
{
AddConflictKey(prevAA, null, true);
AddConflictKey(null, ModTerminus.C, true);
}
}
