private IEnumerable<Bookmark> FindAll(IdentityPath identityPath, DocNode docNode)
{
var results = new List<Bookmark>();
var transitionGroupDocNode = docNode as TransitionGroupDocNode;
if (transitionGroupDocNode == null)
{
var docNodeParent = docNode as DocNodeParent;
if (docNodeParent == null)
{
return results;
}
foreach (var child in docNodeParent.Children)
{
results.AddRange(FindAll(new IdentityPath(identityPath, child.Id), child));
}
return results;
}
if (!transitionGroupDocNode.HasResults)
{
return results;
}
for (int iReplicate = 0; iReplicate < transitionGroupDocNode.Results.Count; iReplicate++)
{
var replicate = transitionGroupDocNode.Results[iReplicate];
if (replicate == null)
{
continue;
}
var fileDatas = new Dictionary<FinderChromFileKey, FinderChromFileData>();
foreach (var transitionGroupChromInfo in replicate)
{
FinderChromFileData chromFileData;
var chromFileKey = new FinderChromFileKey(transitionGroupChromInfo);
if (!fileDatas.TryGetValue(chromFileKey, out chromFileData))
{
chromFileData = new FinderChromFileData
{
TransitionGroupChromInfo = transitionGroupChromInfo,
MatchingTransitionBookmarks = new List<Bookmark>(),
AllTransitionsMatch = true,
};
fileDatas.Add(chromFileKey, chromFileData);
}
}
foreach (var transitionDocNode in transitionGroupDocNode.Transitions)
{
if (!transitionDocNode.HasResults || iReplicate >= transitionDocNode.Results.Count)
{
continue;
}
var transitionResults = transitionDocNode.Results[iReplicate];
if (transitionResults == null)
{
continue;
}
var transitionId = new IdentityPath(identityPath, transitionDocNode.Id);
foreach (var chromInfo in transitionResults)
{
FinderChromFileData chromFileData;
bool match = MatchTransition(chromInfo) != null;
var transitionBookmark = new Bookmark(transitionId, chromInfo.FileId,
chromInfo.OptimizationStep);
var chromFileKey = new FinderChromFileKey(chromInfo);
if (!fileDatas.TryGetValue(chromFileKey, out chromFileData))
{
if (match)
{
results.Add(transitionBookmark);
}
}
else
{
if (match)
{
chromFileData.MatchingTransitionBookmarks.Add(transitionBookmark);
}
else
{
chromFileData.AllTransitionsMatch = false;
}
}
}
}
foreach (var fileDataEntry in fileDatas)
{
if (fileDataEntry.Value.AllTransitionsMatch && fileDataEntry.Value.MatchingTransitionBookmarks.Count > 0)
{
var transitionGroupMatch = MatchTransitionGroup(fileDataEntry.Value.TransitionGroupChromInfo);
if (transitionGroupMatch != null)
{
results.Add(new Bookmark(identityPath, fileDataEntry.Value.TransitionGroupChromInfo.FileId, fileDataEntry.Value.TransitionGroupChromInfo.OptimizationStep));
continue;
}
}
results.AddRange(fileDataEntry.Value.MatchingTransitionBookmarks);
}
}
return results;
}
public Bookmark(Bookmark bookmark)
{
IdentityPath = bookmark.IdentityPath;
ChromFileInfoId = bookmark.ChromFileInfoId;
}
public static Bookmark ToBookmark(DocumentLocation documentLocation, SrmDocument document)
{
Bookmark bookmark = new Bookmark();
if (documentLocation.IdPath.Any())
{
IdentityPath identityPath = IdentityPath.ToIdentityPath(documentLocation.IdPath, document);
if (null == identityPath)
{
throw new ArgumentException("Unable to find target node " + documentLocation.IdPathToString()); // Not L10N
}
bookmark = bookmark.ChangeIdentityPath(identityPath);
}
if (documentLocation.ChromFileId.HasValue)
{
ChromFileInfoId chromFileInfoId = null;
if (document.Settings.HasResults)
{
foreach (var chromatogramSet in document.Settings.MeasuredResults.Chromatograms)
{
var chromFileInfo =
chromatogramSet.MSDataFileInfos.FirstOrDefault(
fileInfo => fileInfo.Id.GlobalIndex == documentLocation.ChromFileId);
if (null != chromFileInfo)
{
chromFileInfoId = chromFileInfo.FileId;
}
}
}
if (null == chromFileInfoId)
{
throw new ArgumentException("Unable to find file id " + documentLocation.ChromFileId); // Not L10N
}
bookmark = bookmark.ChangeChromFileInfoId(chromFileInfoId);
}
if (documentLocation.OptStep.HasValue)
{
bookmark = bookmark.ChangeOptStep(documentLocation.OptStep.Value);
}
return bookmark;
}
public bool Equals(Bookmark other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other.IdentityPath, IdentityPath)
&& ReferenceEquals(other.ChromFileInfoId, ChromFileInfoId)
&& Equals(other.OptStep, OptStep);
}
