public SrmSettings AddCheckedModifications(SrmDocument document)
{
var firstHeavyModificationType = document.Settings.PeptideSettings.Modifications
.GetHeavyModificationTypes().FirstOrDefault();
// in the non-DDA case, AddCheckedModifications is only additive, so no checked items is a no-op
if (modificationsListBox.CheckedItems.Count == 0)
{
if (!ImportPeptideSearch.IsDDASearch)
{
return(document.Settings);
}
else
{
// in DDA-case, return empty mod lists
var emptyPeptideMods = document.Settings.PeptideSettings.Modifications
.ChangeStaticModifications(new List <StaticMod>());
emptyPeptideMods = emptyPeptideMods.ChangeModifications(firstHeavyModificationType, new List <StaticMod>());
return(ImportPeptideSearch.AddModifications(document, emptyPeptideMods));
}
}
// Find checked mods
List <StaticMod> structuralMods;
List <StaticMod> heavyMods;
if (ImportPeptideSearch.IsDDASearch)
{
var selectedMods = modificationsListBox.CheckedItems.Cast <ListBoxModification>().Select(o => o.Mod).ToList();
structuralMods = selectedMods.Where(o => o.LabelAtoms == LabelAtoms.None).ToList();
heavyMods = selectedMods.Where(o => o.LabelAtoms != LabelAtoms.None).ToList();
}
else
{
structuralMods = (from mod in ImportPeptideSearch.MatcherPepMods.StaticModifications
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Find checked heavy mods
heavyMods = (from mod in ImportPeptideSearch.MatcherHeavyMods
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
}
// Update document modifications
var newPeptideMods = document.Settings.PeptideSettings.Modifications.ChangeStaticModifications(structuralMods);
newPeptideMods = newPeptideMods.ChangeModifications(firstHeavyModificationType, heavyMods);
return(ImportPeptideSearch.AddModifications(document, newPeptideMods));
}
public SrmSettings AddCheckedModifications(SrmDocument document)
{
if (modificationsListBox.CheckedItems.Count == 0)
{
return(document.Settings);
}
// Find checked static mods
var newStructuralMods = (from mod in ImportPeptideSearch.MatcherPepMods.StaticModifications
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Find checked heavy mods
var newHeavyMods = (from mod in ImportPeptideSearch.MatcherHeavyMods
from ListBoxModification checkedMod in modificationsListBox.CheckedItems
where mod.Equivalent(checkedMod.Mod)
select mod).ToList();
// Update document modifications
return(ImportPeptideSearch.AddModifications(document,
new PeptideModifications(newStructuralMods, new[] { new TypedModifications(IsotopeLabelType.heavy, newHeavyMods) })));
}