public void AddModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToList();
newMods.Add(mod);
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
else if (labelType.IsLight)
{
MatcherPepMods =
new PeptideModifications(new List <StaticMod> {
mod
}, MatcherPepMods.GetHeavyModifications().ToArray());
}
else
{
var typedHeavyMods =
new List <TypedModifications>(MatcherPepMods.GetHeavyModifications())
{
new TypedModifications(labelType, new List <StaticMod> {
mod
})
};
MatcherPepMods = new PeptideModifications(MatcherPepMods.StaticModifications, typedHeavyMods);
}
MatchesUpdated = true;
}
/// <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)
};
}
}
}
public void RemoveModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToArray();
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
MatchesUpdated = true;
}
/// <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 void OkDialog()
{
StaticMod[] removeStructuralMods, removeHeavyMods;
GetListModifications(CheckState.Unchecked, out removeStructuralMods, out removeHeavyMods);
foreach (var remMod in removeStructuralMods.Concat(removeHeavyMods))
{
foreach (var match in Matcher.Matches.ToArray())
{
if ((match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(remMod)) ||
(match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(remMod)))
{
Matcher.Matches.Remove(match.Key);
}
}
}
MatcherPepMods = MatcherPepMods.ChangeStaticModifications(MatcherPepMods.StaticModifications.Where(mod => !removeStructuralMods.Contains(mod)).ToList());
MatcherPepMods = MatcherPepMods.RemoveHeavyModifications(removeHeavyMods);
DialogResult = DialogResult.OK;
}