private List <KeyValuePair <IList <StaticMod>, int> > CalcApplicableMods(SrmSettings settings, IVariableModFilter filterVariableMod)
{
var mods = settings.PeptideSettings.Modifications;
// Nothing to do, if no variable mods in the document
if (!mods.HasVariableModifications)
{
return(null);
}
// Enumerate each amino acid in the sequence
List <KeyValuePair <IList <StaticMod>, int> > listListMods = null;
int len = Sequence.Length;
for (int i = 0; i < len; i++)
{
if (filterVariableMod != null && !filterVariableMod.IsModIndex(i))
{
continue;
}
char aa = Sequence[i];
bool matchingMods = false;
// Test each modification to see if it applies
foreach (var mod in mods.VariableModifications)
{
if (!mod.IsMod(aa, i, len))
{
continue;
}
// If the modification applies, store it in the list
if (listListMods == null)
{
listListMods = new List <KeyValuePair <IList <StaticMod>, int> >();
}
if (listListMods.Count == 0 || listListMods[listListMods.Count - 1].Value != i)
{
listListMods.Add(new KeyValuePair <IList <StaticMod>, int>(new List <StaticMod>(), i));
}
var listMods = listListMods[listListMods.Count - 1].Key;
if (filterVariableMod == null)
{
listMods.Add(mod);
}
else
{
// If the filter matches, then only allow this one mod
double?modMass = settings.TransitionSettings.Prediction.PrecursorMassType == MassType.Monoisotopic
? mod.MonoisotopicMass
: mod.AverageMass;
if (modMass.HasValue && filterVariableMod.IsModMass(i, modMass.Value))
{
// Clear all non-matching mods when the first match is found
if (!matchingMods)
{
listMods.Clear();
}
matchingMods = true;
}
else if (matchingMods)
{
continue; // Skip non-matching mods if matching
}
listMods.Add(mod);
}
}
}
return(listListMods);
}
public IEnumerable <PeptideDocNode> CreateDocNodes(SrmSettings settings, IPeptideFilter filter, IVariableModFilter filterVariableMod = null)
{
int maxModCount = filter.MaxVariableMods ?? settings.PeptideSettings.Modifications.MaxVariableMods;
// Always return the unmodified peptide doc node first
var nodePepUnmod = new PeptideDocNode(this);
bool allowVariableMods;
if (filter.Accept(settings, this, null, out allowVariableMods))
{
yield return(nodePepUnmod);
}
// Stop if no variable modifications are allowed for this peptide.
if (!allowVariableMods || maxModCount == 0)
{
yield break;
}
// First build a list of the amino acids in this peptide which can be modified,
// and the modifications which apply to them.
var listListMods = CalcApplicableMods(settings, filterVariableMod);
// If no applicable modifications were found, return a single DocNode for the
// peptide passed in
if (listListMods == null)
{
yield break;
}
maxModCount = Math.Min(maxModCount, listListMods.Count);
for (int modCount = 1; modCount <= maxModCount; modCount++)
{
var modStateMachine = new VariableModStateMachine(nodePepUnmod, modCount, listListMods);
foreach (var nodePep in modStateMachine.GetStates())
{
if (filter.Accept(settings, nodePep.Peptide, nodePep.ExplicitMods, out allowVariableMods))
{
yield return(nodePep);
}
}
}
}
