/// <summary>
/// Make all heavy modifications explicit. The document insert code will force them
/// back to implicit later, if the match the implicit modifications.
/// </summary>
public void ConvertAllHeavyModsExplicit()
{
foreach (var typedModifications in MatcherPepMods.GetHeavyModifications())
{
MatcherPepMods = MatcherPepMods.ChangeModifications(typedModifications.LabelType,
typedModifications.Modifications.Select(mod =>
{
if (UserDefinedTypedMods.Keys.Any(userMod => userMod.Equivalent(mod)))
{
return(mod);
}
return(mod.ChangeExplicit(true));
}).ToArray());
}
foreach (var key in Matches.Keys.ToArray())
{
var match = Matches[key];
if (match.HeavyMod != null && !UserDefinedTypedMods.Keys.Contains(match.HeavyMod))
{
Matches[key] = new AAModMatch
{
StructuralMod = match.StructuralMod,
HeavyMod = match.HeavyMod.ChangeExplicit(true)
};
}
}
}
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);
}
/// <summary>
/// Make all heavy modifications explicit. The document insert code will force them
/// back to implicit later, if the match the implicit modifications.
/// </summary>
public void ConvertAllHeavyModsExplicit()
{
MatcherPepMods = MatcherPepMods.ChangeHeavyModifications(MatcherPepMods.HeavyModifications.Select(
mod =>
UserDefinedTypedMods.Keys.Contains(userMod => userMod.Equivalent(mod))
? mod
: mod.ChangeExplicit(true)).ToArray());
foreach (var key in Matches.Keys.ToArray())
{
var match = Matches[key];
if (match.HeavyMod != null && !UserDefinedTypedMods.Keys.Contains(match.HeavyMod))
{
Matches[key] = new AAModMatch
{
StructuralMod = match.StructuralMod,
HeavyMod = match.HeavyMod.ChangeExplicit(true)
};
}
}
}
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);
}
}
/// <summary>
/// Make all heavy modifications explicit. The document insert code will force them
/// back to implicit later, if the match the implicit modifications.
/// </summary>
public void ConvertAllHeavyModsExplicit()
{
MatcherPepMods = MatcherPepMods.ChangeHeavyModifications(MatcherPepMods.HeavyModifications.Select(
mod =>
UserDefinedTypedMods.Keys.Contains(userMod => userMod.Equivalent(mod))
? mod
: mod.ChangeExplicit(true)).ToArray());
foreach (var key in Matches.Keys.ToArray())
{
var match = Matches[key];
if (match.HeavyMod != null && !UserDefinedTypedMods.Keys.Contains(match.HeavyMod))
{
Matches[key] = new AAModMatch
{
StructuralMod = match.StructuralMod,
HeavyMod = match.HeavyMod.ChangeExplicit(true)
};
}
}
}
public PeptideDocNode CreateDocNodeFromMatches(PeptideDocNode nodePep, IEnumerable <AAModInfo> infos, bool stringPaste, out bool hasHeavy)
{
hasHeavy = false;
List <ExplicitMod> listLightMods = new List <ExplicitMod>();
var dictHeavyMods = new Dictionary <IsotopeLabelType, List <ExplicitMod> >();
foreach (var info in infos)
{
var match = GetMatch(info.ModKey);
if (match == null)
{
return(null);
}
AAModMatch modMatch = (AAModMatch)match;
var lightMod = modMatch.StructuralMod;
if (lightMod != null)
{
// Make sure all mods are explicit for ensure mods.
if (stringPaste)
{
lightMod = lightMod.ChangeExplicit(true);
}
listLightMods.Add(new ExplicitMod(info.IndexAA, lightMod));
}
var heavyMod = modMatch.HeavyMod;
if (heavyMod != null)
{
var type = UserDefinedTypedMods.ContainsKey(modMatch.HeavyMod)
? UserDefinedTypedMods[modMatch.HeavyMod]
: DocDefHeavyLabelType;
List <ExplicitMod> listHeavyMods;
if (!dictHeavyMods.TryGetValue(type, out listHeavyMods))
{
listHeavyMods = new List <ExplicitMod>();
dictHeavyMods.Add(type, listHeavyMods);
}
listHeavyMods.Add(new ExplicitMod(info.IndexAA, heavyMod));
}
}
// Build the set of explicit modifications for the peptide.
// If ensure mods is set to true, then perform the work here to ensure
// that the mods persist corectly with the current settings.
var targetImplicitMods = new ExplicitMods(nodePep,
Settings.PeptideSettings.Modifications.StaticModifications,
DefSetStatic,
Settings.PeptideSettings.Modifications.GetHeavyModifications(),
DefSetHeavy);
// If no light modifications are present, this code assumes the user wants the
// default global light modifications. Unless not stringPaste, in which case the target
// static mods must also be empty
if (listLightMods.Count == 0 && (stringPaste || targetImplicitMods.StaticModifications.Count == 0))
{
listLightMods = null;
}
else if (stringPaste && ArrayUtil.EqualsDeep(listLightMods.ToArray(), targetImplicitMods.StaticModifications))
{
listLightMods = null;
}
var listTypedHeavyMods = new List <TypedExplicitModifications>();
foreach (var targetDocMod in targetImplicitMods.GetHeavyModifications())
{
List <ExplicitMod> listMods;
if (dictHeavyMods.TryGetValue(targetDocMod.LabelType, out listMods) &&
(!stringPaste || !ArrayUtil.EqualsDeep(listMods, targetDocMod.Modifications)))
{
listTypedHeavyMods.Add(new TypedExplicitModifications(nodePep.Peptide, targetDocMod.LabelType, listMods)
.AddModMasses(listLightMods == null ? null : new TypedExplicitModifications(nodePep.Peptide, IsotopeLabelType.light, listLightMods)));
}
}
// Put the explicit modifications on the peptide.
ExplicitMods mods = (listLightMods != null || listTypedHeavyMods.Count > 0)
? new ExplicitMods(nodePep.Peptide, listLightMods, listTypedHeavyMods,
listLightMods != null && listLightMods.Contains(mod => mod.Modification.IsVariable))
: null;
hasHeavy = dictHeavyMods.Keys.Count > 0;
return(nodePep.ChangeExplicitMods(mods).ChangeSettings(Settings, SrmSettingsDiff.PROPS));
}
private void AddMatch(AAModKey key, AAModMatch match)
{
Matches.Add(key, match);
}
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;
}
private void AddMatch(AAModKey key, AAModMatch match)
{
Matches.Add(key, match);
}
public abstract void UpdateMatcher(AAModInfo info, AAModMatch? match);
public override void UpdateMatcher(AAModInfo info, AAModMatch? match)
{
if(match == null)
{
var unmatchedSeq = GetSeqModUnmatchedStr(info.IndexAAInSeq);
if (!UnmatchedSequences.Contains(unmatchedSeq))
UnmatchedSequences.Add(unmatchedSeq);
}
}
