public SrmDocument ChangePeak(SrmDocument doc, SrmTreeNode nodePepTree, TransitionGroupDocNode nodeTranGroup, string nameSet, MsDataFileUri filePath)
{
if ((_retentionTime ?? StartTime) == null)
{
return(doc);
}
var groupPath = new IdentityPath(nodePepTree.Path, nodeTranGroup.Id);
doc = _retentionTime.HasValue
? doc.ChangePeak(groupPath, nameSet, filePath, null, _retentionTime.Value, UserSet.TRUE)
: doc.ChangePeak(groupPath, nameSet, filePath, null, StartTime, EndTime, UserSet.TRUE, null, false);
var activeTransitionGroup = (TransitionGroupDocNode)doc.FindNode(groupPath);
if (activeTransitionGroup.RelativeRT != RelativeRT.Matching)
{
return(doc);
}
var activeChromInfo = SkylineWindow.FindChromInfo(doc, activeTransitionGroup, nameSet, filePath);
var peptide = (PeptideDocNode)doc.FindNode(groupPath.Parent);
// See if there are any other transition groups that should have their peak bounds set to the same value
foreach (var tranGroup in peptide.TransitionGroups.Where(tranGroup => tranGroup.RelativeRT == RelativeRT.Matching))
{
var otherGroupPath = new IdentityPath(groupPath.Parent, tranGroup.TransitionGroup);
if (Equals(groupPath, otherGroupPath) || SkylineWindow.FindChromInfo(doc, tranGroup, nameSet, filePath) == null)
{
continue;
}
doc = doc.ChangePeak(otherGroupPath, nameSet, filePath, null,
activeChromInfo.StartRetentionTime, activeChromInfo.EndRetentionTime, UserSet.TRUE, activeChromInfo.Identified, false);
}
return(doc);
}