public List <TypedExplicitModifications> PermuteTypedExplicitModifications(IList <IsotopeLabelType> partialLabelTypes, PeptideDocNode peptideDocNode, IList <int> potentiallyModifiedResidues)
{
var typedExplicitMods = new List <TypedExplicitModifications>();
List <ImmutableList <int> > permutations;
if (SimplePermutation)
{
permutations = GenerateSimplePermutations(potentiallyModifiedResidues).ToList();
}
else
{
permutations = GenerateComplexPermutations(potentiallyModifiedResidues).ToList();
}
for (int i = 1; i < permutations.Count; i++)
{
IsotopeLabelType labelType;
if (i == permutations.Count - 1)
{
labelType = FullyHeavyLabelType;
}
else
{
labelType = partialLabelTypes[i];
}
var explicitMods = permutations[i].Select(indexAA => new ExplicitMod(indexAA, IsotopeModification)).ToList();
var typedMods = new TypedExplicitModifications(peptideDocNode.Peptide, labelType, explicitMods);
typedExplicitMods.Add(typedMods);
}
return(typedExplicitMods);
}
public void OkDialog()
{
var peptide = NodePeptide.Peptide;
var explicitModsCurrent = NodePeptide.ExplicitMods;
var modsDoc = DocSettings.PeptideSettings.Modifications;
var implicitMods = new ExplicitMods(NodePeptide,
modsDoc.StaticModifications, Settings.Default.StaticModList,
modsDoc.GetHeavyModifications(), Settings.Default.HeavyModList);
// Get static modifications from the dialog, and check for equality with
// the document implicit modifications.
TypedExplicitModifications staticTypedMods = null;
bool isVariableStaticMods = false;
var staticMods = GetExplicitMods(_listComboStatic, Settings.Default.StaticModList);
if (ArrayUtil.EqualsDeep(staticMods, implicitMods.StaticModifications))
{
if (!NodePeptide.HasVariableMods)
{
staticMods = null; // Use implicit modifications
}
else
{
staticMods = explicitModsCurrent.StaticModifications;
isVariableStaticMods = true;
}
}
else if (explicitModsCurrent != null &&
ArrayUtil.EqualsDeep(staticMods, explicitModsCurrent.StaticModifications))
{
staticMods = explicitModsCurrent.StaticModifications;
}
if (staticMods != null)
{
staticTypedMods = new TypedExplicitModifications(peptide,
IsotopeLabelType.light, staticMods);
}
var listHeavyTypedMods = new List <TypedExplicitModifications>();
for (int i = 0; i < _listLabelTypeHeavy.Count; i++)
{
var labelType = _listLabelTypeHeavy[i];
var heavyMods = GetExplicitMods(_listListComboHeavy[i], Settings.Default.HeavyModList);
if (ArrayUtil.EqualsDeep(heavyMods, implicitMods.GetModifications(labelType)))
{
continue;
}
var heavyTypedMods = new TypedExplicitModifications(peptide, labelType, heavyMods);
listHeavyTypedMods.Add(heavyTypedMods.AddModMasses(staticTypedMods));
}
ExplicitMods explicitMods = null;
if (staticMods != null || listHeavyTypedMods.Count > 0)
{
explicitMods = new ExplicitMods(peptide, staticMods, listHeavyTypedMods, isVariableStaticMods);
}
Helpers.AssignIfEquals(ref explicitMods, explicitModsCurrent);
ExplicitMods = explicitMods;
DialogResult = DialogResult.OK;
Close();
}
