public PeptideDocNode CreateDocNodeFromSettings(string seq, Peptide peptide, SrmSettingsDiff diff,
out TransitionGroupDocNode nodeGroupMatched)
{
seq = Transition.StripChargeIndicators(seq, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE);
if (peptide == null)
{
string seqUnmod = FastaSequence.StripModifications(seq);
try
{
peptide = new Peptide(null, seqUnmod, null, null,
Settings.PeptideSettings.Enzyme.CountCleavagePoints(seqUnmod));
}
catch (InvalidDataException)
{
nodeGroupMatched = null;
return(null);
}
}
// Use the number of modifications as the maximum, if it is less than the current
// settings to keep from over enumerating, which can be slow.
var filter = new MaxModFilter(Math.Min(seq.Count(c => c == '[' || c == '('),
Settings.PeptideSettings.Modifications.MaxVariableMods));
foreach (var nodePep in peptide.CreateDocNodes(Settings, filter))
{
var nodePepMod = CreateDocNodeFromSettings(seq, nodePep, diff, out nodeGroupMatched);
if (nodePepMod != null)
{
return(nodePepMod);
}
}
nodeGroupMatched = null;
return(null);
}
public PeptideDocNode CreateDocNodeFromSettings(string seq, Peptide peptide, SrmSettingsDiff diff,
out TransitionGroupDocNode nodeGroupMatched)
{
seq = Transition.StripChargeIndicators(seq, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE);
if (peptide == null)
{
string seqUnmod = FastaSequence.StripModifications(seq);
try
{
peptide = new Peptide(null, seqUnmod, null, null,
Settings.PeptideSettings.Enzyme.CountCleavagePoints(seqUnmod));
}
catch (InvalidDataException)
{
nodeGroupMatched = null;
return null;
}
}
// Use the number of modifications as the maximum, if it is less than the current
// settings to keep from over enumerating, which can be slow.
var filter = new MaxModFilter(Math.Min(seq.Count(c => c == '[' || c == '('),
Settings.PeptideSettings.Modifications.MaxVariableMods));
foreach (var nodePep in peptide.CreateDocNodes(Settings, filter))
{
var nodePepMod = CreateDocNodeFromSettings(seq, nodePep, diff, out nodeGroupMatched);
if (nodePepMod != null)
return nodePepMod;
}
nodeGroupMatched = null;
return null;
}
