/// <summary>
/// Create PeptideModifications matching the modifications indicated in the library.
/// </summary>
/// <param name="settings">The settings for the document for which the matches will be made</param>
public PeptideModifications CreateMatcherPeptideSettings(SrmSettings settings)
{
var lightMods = new List <StaticMod>();
var heavyMods = new Dictionary <IsotopeLabelType, List <StaticMod> >();
if (HasMatches)
{
foreach (var matchPair in Matches)
{
var structuralMod = matchPair.Value.StructuralMod;
StaticMod mod1 = structuralMod;
if (structuralMod != null && !lightMods.Contains(mod => mod.Equivalent(mod1)))
{
// Make all found structural mods variable, unless they are preexisting modifications.
if (!UserDefinedTypedMods.ContainsKey(structuralMod) || structuralMod.IsUserSet)
{
structuralMod = structuralMod.ChangeVariable(true);
}
// Set modification to be implicit if it appears to be implicit in the library.
if (!UserDefinedTypedMods.ContainsKey(structuralMod) && !IsVariableMod(structuralMod))
{
structuralMod = structuralMod.ChangeExplicit(false);
}
lightMods.Add(structuralMod);
}
var heavyMod = matchPair.Value.HeavyMod;
if (heavyMod == null)
{
continue;
}
IsotopeLabelType labelType;
if (!UserDefinedTypedMods.TryGetValue(heavyMod, out labelType))
{
labelType = DocDefHeavyLabelType;
}
heavyMod = heavyMod.ChangeExplicit(false);
if (!heavyMods.ContainsKey(labelType))
{
heavyMods.Add(labelType, new List <StaticMod> {
heavyMod
});
}
else if (!heavyMods[labelType].Contains(mod => mod.Equivalent(heavyMod)))
{
heavyMods[labelType].Add(heavyMod);
}
}
}
var typedModifications = new List <TypedModifications>();
foreach (var labelType in heavyMods.Keys)
{
typedModifications.Add(new TypedModifications(labelType, heavyMods[labelType]));
}
var mods = settings.PeptideSettings.Modifications;
return(new PeptideModifications(lightMods, mods.MaxVariableMods, mods.MaxNeutralLosses,
typedModifications, new[] { IsotopeLabelType.heavy }));
}
