/// <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));
}
/// <summary>
/// Change the format of all modifications so that they are in the Skyline 3.7
/// format of having one digit after the decimal.
/// </summary>
public PeptideLibraryKey FormatToOneDecimal()
{
if (!HasModifications)
{
return(this);
}
StringBuilder newSequence = new StringBuilder();
int aaCount = 0;
foreach (var mod in GetModifications())
{
newSequence.Append(UnmodifiedSequence.Substring(aaCount, mod.Key + 1 - aaCount));
aaCount = mod.Key + 1;
var massModification = MassModification.Parse(mod.Value);
string newMod;
if (massModification == null)
{
newMod = mod.Value;
}
else
{
newMod = new MassModification(massModification.Mass, 1).ToString();
}
newSequence.Append(Model.ModifiedSequence.Bracket(newMod));
}
newSequence.Append(UnmodifiedSequence.Substring(aaCount));
return(new PeptideLibraryKey(newSequence.ToString(), Charge));
}
public StaticMod ClosestMatchGeneral(MassModification massModification, ModTerminus?terminus)
{
StaticMod match = ClosestMatch(_listAllAAsMasses, massModification);
if (match == null && terminus != null)
{
match = ClosestMatch(terminus == ModTerminus.C ? _listCTerminalMasses : _listNTerminalMasses, massModification);
}
return(match ?? ClosestMatch(_listMasses, massModification));
}
public StaticMod ClosestMatchSpecific(MassModification massModification, ModTerminus?terminus)
{
// Order of preference: matches that specific amino acids
StaticMod match = ClosestMatch(_listMasses, massModification);
// Terminal matches
if (match == null && terminus != null)
{
match = ClosestMatch(terminus == ModTerminus.C ? _listCTerminalMasses : _listNTerminalMasses, massModification);
}
// Matches that apply to all amino acids
return(match ?? ClosestMatch(_listAllAAsMasses, massModification));
}
public static bool ModificationsMatch(string strMod1, string strMod2)
{
if (strMod1 == strMod2)
{
return(true);
}
var massMod1 = MassModification.Parse(strMod1);
var massMod2 = MassModification.Parse(strMod2);
if (massMod1 == null || massMod2 == null)
{
return(false);
}
return(massMod1.Matches(massMod2));
}
private static StaticMod ClosestMatch(List <KeyValuePair <double, StaticMod> > listSearch, MassModification massModification)
{
if (listSearch.Count == 0)
{
return(null);
}
int i = listSearch.BinarySearch(new KeyValuePair <double, StaticMod>(massModification.Mass, null), MASS_COMPARER);
i = i < 0 ? ~i : i;
var match = listSearch[i == listSearch.Count ? i - 1 : i];
if (massModification.Matches(new MassModification(match.Key, UniMod.UNIMOD_PRECISION)))
{
return(match.Value);
}
if (i > 0)
{
match = listSearch[i - 1];
if (massModification.Matches(new MassModification(match.Key, UniMod.UNIMOD_PRECISION)))
{
return(match.Value);
}
}
return(null);
}
public StaticMod ClosestMatch(MassModification massModification, ModTerminus?terminus, bool specific)
{
return(specific
? ClosestMatchSpecific(massModification, terminus)
: ClosestMatchGeneral(massModification, terminus));
}
