private StaticMod GetModByMassInSettings(AAModInfo info, double mass, bool structural)
{
StaticMod firstMatch = null;
foreach (var match in EnumerateModMatchesInSettings(info, mass, structural))
{
firstMatch = firstMatch ?? match;
// Keep looking if it is an isotope modification of the 15N variant where it applies to all amino acids
if (structural || (info.AppearsToBeSpecificMod && (!string.IsNullOrEmpty(match.AAs) || match.Terminus != null)) ||
(!info.AppearsToBeSpecificMod && string.IsNullOrEmpty(match.AAs) && match.Terminus == null))
{
firstMatch = match;
break;
}
}
if (firstMatch == null)
{
return(null);
}
// TODO: Is this necessary
if (!IsInSettings(firstMatch) && !firstMatch.IsVariable)
{
firstMatch = firstMatch.ChangeExplicit(true);
}
return(firstMatch);
}
private IEnumerable <StaticMod> EnumerateModMatchesInSettings(AAModInfo info, double mass, bool structural)
{
var modifications = Settings.PeptideSettings.Modifications;
foreach (var type in modifications.GetModificationTypes())
{
foreach (var mod in modifications.GetModifications(type)
.Where(mod => info.IsMassMatch(mod, mass)))
{
if (type.IsLight == structural)
{
yield return(mod);
}
}
}
if (!structural)
{
foreach (var mod in DefSetHeavy.Where(mod => info.IsMassMatch(mod, mass)))
{
yield return(mod);
}
}
else
{
foreach (var mod in DefSetStatic.Where(mod => info.IsMassMatch(mod, mass)))
{
yield return(mod);
}
}
}
private AAModMatch?GetModByName(AAModInfo info)
{
bool structural = false;
StaticMod modMatch = null;
// First, look in the document/global settings.
foreach (var mod in UserDefinedTypedMods.Keys)
{
bool matchStuctural = UserDefinedTypedMods[mod].IsLight;
if (Equals(info.Name, mod.Name) &&
(!info.UserIndicatedHeavy || !matchStuctural))
{
modMatch = mod;
structural = matchStuctural;
}
}
// If not found, then look in Unimod.
modMatch = modMatch ?? UniMod.GetModification(info.Name, out structural);
if (!info.IsModMatch(modMatch) || (info.UserIndicatedHeavy && structural))
{
return(null);
}
return(new AAModMatch
{
StructuralMod = structural ? modMatch : null,
HeavyMod = !structural ? modMatch : null
});
}
public override void UpdateMatcher(AAModInfo info, AAModMatch?match)
{
if (match == null)
{
var unmatchedSeq = GetSeqModUnmatchedStr(info.IndexAAInSeq);
if (!UnmatchedSequences.Contains(unmatchedSeq))
{
UnmatchedSequences.Add(unmatchedSeq);
}
}
}
private AAModMatch?GetModByMass(AAModInfo info)
{
AAModMatch?match = null;
// Enumerate all possible partial matches for the given AAModInfo, looking for
// a complete match for the mass.
foreach (var partialMatch in SearchPartialModMatches(info))
{
// If a partial match explains the entire mass, it is a complete match, so the search is done.
if (partialMatch.UnexplainedMass == 0)
{
return new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : null,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : null
}
}
;
// Otherwise, first try to complete the match by looking in the document modifications and
// global modifications.
var matchComplete = GetModByMassInSettings(info, partialMatch.UnexplainedMass, !partialMatch.Structural);
if (matchComplete != null)
{
// If we complete the match with a modification in the document or global settings,
// return that match.
return(new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : matchComplete,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : matchComplete
});
}
// If we already have found a potential match in Unimod, don't continue searching Unimod.
if (match != null)
{
continue;
}
// Look in Unimod to complete the match.
matchComplete = UniMod.MassLookup.MatchModificationMass(partialMatch.UnexplainedMass, info.AA,
info.RoundedTo, !partialMatch.Structural,
info.Terminus, info.AppearsToBeSpecificMod);
if (matchComplete != null)
{
// A match that is partially explained by unimod is not as good as a match in the document/gobals,
// so keep this match as a good candidate, but keep searching.
match = new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : matchComplete,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : matchComplete
};
}
}
return(match);
}
EnumeratePartialModMatches(Dictionary <IEnumerable <StaticMod>, bool> dictModLists,
AAModInfo info)
{
foreach (var dict in dictModLists)
{
var mods = dict.Key;
// Mod can be null to force search for only light/heavy match.
foreach (var mod in mods.Where(mod => mod == null || info.IsModMatch(mod)))
{
double modMass = mod == null ? 0 : GetDefaultModMass(info.AA, mod);
double mass = (info.Mass ?? 0) - modMass;
yield return(new PartialMassMatch
{
Mod = mod == null ? null : mod.ChangeExplicit(true),
Structural = dict.Value,
UnexplainedMass = Math.Round(mass,
info.RoundedTo)
});
}
}
}
/// <summary>
/// Enumerates partial modifications matches for the given AAModInfo.
///
/// Enumerate matches in the following order:
/// 1. Partials matches for any previously matched heavy labeling.
/// 2. Partial structural match with a null structural modification, this means that any complete match
/// would have only a heavy modification.
/// 3. Partial heavy match with a null heavy modification.
/// 4. Partial matches from the document settings.
/// 5. Partial heavy matches from UniMod.
/// 6. Partial heavy matches from UniMod (hidden).
/// </summary>
private IEnumerable <PartialMassMatch> SearchPartialModMatches(AAModInfo info)
{
Dictionary <IEnumerable <StaticMod>, bool> listsToSearch = new Dictionary <IEnumerable <StaticMod>, bool>();
if (!info.AppearsToBeSpecificMod)
{
listsToSearch.Add(_foundHeavyLabels, false);
}
listsToSearch.Add(new StaticMod[] { null }, true);
listsToSearch.Add(new StaticMod[] { null }, false);
foreach (var labelType in Settings.PeptideSettings.Modifications.GetModificationTypes())
{
listsToSearch.Add(Settings.PeptideSettings.Modifications.GetModifications(labelType).ToArray(),
labelType.IsLight);
}
listsToSearch.Add(DefSetStatic, true);
listsToSearch.Add(DefSetHeavy, false);
listsToSearch.Add(UniMod.DictIsotopeModNames.Values, false);
listsToSearch.Add(UniMod.DictHiddenIsotopeModNames.Values, false);
return(EnumeratePartialModMatches(listsToSearch, info));
}
public override void UpdateMatcher(AAModInfo info, AAModMatch?match)
{
// Update unmatched sequences.
if (match == null && !UnmatchedSequences.Contains(info.ModKey.ToString()))
{
UnmatchedSequences.Add(info.ModKey.ToString());
}
if (match == null || match.Value.StructuralMod == null)
{
return;
}
// Update the conflicting mod array.
if (!string.IsNullOrEmpty(match.Value.StructuralMod.AAs))
{
AddConflictKey((byte)info.AA, info.Terminus, false);
}
if (info.Terminus != null)
{
AddConflictKey(null, info.Terminus, false);
}
}
public override void UpdateMatcher(AAModInfo info, AAModMatch? match)
{
if(match == null)
{
var unmatchedSeq = GetSeqModUnmatchedStr(info.IndexAAInSeq);
if (!UnmatchedSequences.Contains(unmatchedSeq))
UnmatchedSequences.Add(unmatchedSeq);
}
}
public override void UpdateMatcher(AAModInfo info, AAModMatch? match)
{
// Update unmatched sequences.
if (match == null && !UnmatchedSequences.Contains(info.ModKey.ToString()))
UnmatchedSequences.Add(info.ModKey.ToString());
if (match == null || match.Value.StructuralMod == null)
return;
// Update the conflicting mod array.
if (!string.IsNullOrEmpty(match.Value.StructuralMod.AAs))
{
AddConflictKey((byte) info.AA, info.Terminus, false);
}
if (info.Terminus != null)
{
AddConflictKey(null, info.Terminus, false);
}
}
private static IEnumerable<PartialMassMatch> EnumeratePartialModMatches(Dictionary<IEnumerable<StaticMod>, bool> dictModLists,
AAModInfo info)
{
foreach (var dict in dictModLists)
{
var mods = dict.Key;
// Mod can be null to force search for only light/heavy match.
foreach (var mod in mods.Where(mod => mod == null || info.IsModMatch(mod)))
{
double modMass = mod == null ? 0 : GetDefaultModMass(info.AA, mod);
double mass = (info.Mass ?? 0) - modMass;
yield return new PartialMassMatch
{
Mod = mod == null ? null : mod.ChangeExplicit(true),
Structural = dict.Value,
UnexplainedMass = Math.Round(mass,
info.RoundedTo)
};
}
}
}
private IEnumerable<StaticMod> EnumerateModMatchesInSettings(AAModInfo info, double mass, bool structural)
{
var modifications = Settings.PeptideSettings.Modifications;
foreach (var type in modifications.GetModificationTypes())
{
foreach (var mod in modifications.GetModifications(type)
.Where(mod => info.IsMassMatch(mod, mass)))
{
if (type.IsLight == structural)
yield return mod;
}
}
if (!structural)
{
foreach (var mod in DefSetHeavy.Where(mod => info.IsMassMatch(mod, mass)))
{
yield return mod;
}
}
else
{
foreach (var mod in DefSetStatic.Where(mod => info.IsMassMatch(mod, mass)))
{
yield return mod;
}
}
}
public abstract void UpdateMatcher(AAModInfo info, AAModMatch? match);
public abstract void UpdateMatcher(AAModInfo info, AAModMatch?match);
/// <summary>
/// Enumerates partial modifications matches for the given AAModInfo.
///
/// Enumerate matches in the following order:
/// 1. Partials matches for any previously matched heavy labeling.
/// 2. Partial structural match with a null structural modification, this means that any complete match
/// would have only a heavy modification.
/// 3. Partial heavy match with a null heavy modification.
/// 4. Partial matches from the document settings.
/// 5. Partial heavy matches from UniMod.
/// 6. Partial heavy matches from UniMod (hidden).
/// </summary>
private IEnumerable<PartialMassMatch> SearchPartialModMatches(AAModInfo info)
{
Dictionary<IEnumerable<StaticMod>, bool> listsToSearch = new Dictionary<IEnumerable<StaticMod>, bool>();
if(!info.AppearsToBeSpecificMod)
listsToSearch.Add(_foundHeavyLabels, false);
listsToSearch.Add(new StaticMod[] { null }, true);
listsToSearch.Add(new StaticMod[] { null }, false);
foreach (var labelType in Settings.PeptideSettings.Modifications.GetModificationTypes())
{
listsToSearch.Add(Settings.PeptideSettings.Modifications.GetModifications(labelType).ToArray(),
labelType.IsLight);
}
listsToSearch.Add(DefSetStatic, true);
listsToSearch.Add(DefSetHeavy, false);
listsToSearch.Add(UniMod.DictIsotopeModNames.Values, false);
listsToSearch.Add(UniMod.DictHiddenIsotopeModNames.Values, false);
return EnumeratePartialModMatches(listsToSearch, info);
}
private AAModMatch? GetModByName(AAModInfo info)
{
bool structural = false;
StaticMod modMatch = null;
// First, look in the document/global settings.
foreach (var mod in UserDefinedTypedMods.Keys)
{
bool matchStuctural = UserDefinedTypedMods[mod].IsLight;
if (Equals(info.Name, mod.Name) &&
(!info.UserIndicatedHeavy || !matchStuctural))
{
modMatch = mod;
structural = matchStuctural;
}
}
// If not found, then look in Unimod.
modMatch = modMatch ?? UniMod.GetModification(info.Name, out structural);
if (!info.IsModMatch(modMatch) || (info.UserIndicatedHeavy && structural))
return null;
return new AAModMatch
{
StructuralMod = structural ? modMatch : null,
HeavyMod = !structural ? modMatch : null
};
}
private StaticMod GetModByMassInSettings(AAModInfo info, double mass, bool structural)
{
StaticMod firstMatch = null;
foreach (var match in EnumerateModMatchesInSettings(info, mass, structural))
{
firstMatch = firstMatch ?? match;
// Keep looking if it is an isotope modification of the 15N variant where it applies to all amino acids
if (structural || (info.AppearsToBeSpecificMod && (!string.IsNullOrEmpty(match.AAs) || match.Terminus != null))
|| (!info.AppearsToBeSpecificMod && string.IsNullOrEmpty(match.AAs) && match.Terminus == null))
{
firstMatch = match;
break;
}
}
if (firstMatch == null)
return null;
// TODO: Is this necessary
if (!IsInSettings(firstMatch) && !firstMatch.IsVariable)
firstMatch = firstMatch.ChangeExplicit(true);
return firstMatch;
}
private AAModMatch? GetModByMass(AAModInfo info)
{
AAModMatch? match = null;
// Enumerate all possible partial matches for the given AAModInfo, looking for
// a complete match for the mass.
foreach (var partialMatch in SearchPartialModMatches(info))
{
// If a partial match explains the entire mass, it is a complete match, so the search is done.
if (partialMatch.UnexplainedMass == 0)
return new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : null,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : null
};
// Otherwise, first try to complete the match by looking in the document modifications and
// global modifications.
var matchComplete = GetModByMassInSettings(info, partialMatch.UnexplainedMass, !partialMatch.Structural);
if (matchComplete != null)
{
// If we complete the match with a modification in the document or global settings,
// return that match.
return new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : matchComplete,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : matchComplete
};
}
// If we already have found a potential match in Unimod, don't continue searching Unimod.
if (match != null)
continue;
// Look in Unimod to complete the match.
matchComplete = UniMod.MassLookup.MatchModificationMass(partialMatch.UnexplainedMass, info.AA,
info.RoundedTo, !partialMatch.Structural,
info.Terminus, info.AppearsToBeSpecificMod);
if (matchComplete != null)
{
// A match that is partially explained by unimod is not as good as a match in the document/gobals,
// so keep this match as a good candidate, but keep searching.
match = new AAModMatch
{
StructuralMod = partialMatch.Structural ? partialMatch.Mod : matchComplete,
HeavyMod = !partialMatch.Structural ? partialMatch.Mod : matchComplete
};
}
}
return match;
}