public PeptideDocNode GetModifiedNode(LibKey key, SrmSettings settings, SrmSettingsDiff diff)
{
var smallMoleculeKey = key.LibraryKey as MoleculeLibraryKey;
var peptideKey = key.LibraryKey as PeptideLibraryKey;
Peptide peptide;
if (smallMoleculeKey != null)
{
peptide = new Peptide(CustomMolecule.FromSmallMoleculeLibraryAttributes(smallMoleculeKey.SmallMoleculeLibraryAttributes));
}
else if (peptideKey != null)
{
peptide = new Peptide(null, peptideKey.UnmodifiedSequence, null, null,
settings.PeptideSettings.Enzyme.CountCleavagePoints(peptideKey.UnmodifiedSequence));
}
else
{
return(null);
}
// First try and create the match from the settings created to match the library explorer.
Settings = HasMatches
? settings.ChangePeptideModifications(mods => MatcherPepMods)
: settings;
TransitionGroupDocNode nodeGroup;
var nodePep = CreateDocNodeFromSettings(key, peptide, diff, out nodeGroup);
if (nodePep != null)
{
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
else
{
// Keep only the matching transition group, so that modifications
// will be highlighted differently for light and heavy forms.
// Only performed when getting peptides for display in the explorer.
nodePep = (PeptideDocNode)nodePep.ChangeChildrenChecked(
new DocNode[] { nodeGroup });
}
return(nodePep);
}
else if (Matches == null)
{
return(null);
}
bool hasHeavy;
// Create explicit mods from the found matches.
nodePep = CreateDocNodeFromMatches(new PeptideDocNode(peptide),
EnumerateSequenceInfos(key.LibraryKey as PeptideLibraryKey, true), false, out hasHeavy);
if (nodePep == null)
{
return(null);
}
// Call change settings with the matched modification settings to enumerate the children.
nodePep = nodePep.ChangeSettings(settings.ChangePeptideModifications(mods =>
!HasMatches ? settings.PeptideSettings.Modifications : MatcherPepMods), diff ?? SrmSettingsDiff.ALL);
if (nodePep.Children.Count == 0)
{
return(null);
}
// Select the correct child, only for use with the library explorer.
if (diff != null && nodePep.Children.Count > 1)
{
nodePep =
(PeptideDocNode)
nodePep.ChangeChildrenChecked(new List <DocNode> {
nodePep.Children[hasHeavy ? 1 : 0]
});
}
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
return(nodePep);
}
public Target(SmallMoleculeLibraryAttributes molecule)
{
Molecule = CustomMolecule.FromSmallMoleculeLibraryAttributes(molecule);
}