public FindResult FindNext(BookmarkEnumerator bookmarkEnumerator)
{
var customMatches = new Dictionary <Bookmark, FindMatch>();
foreach (var finder in FindOptions.CustomFinders)
{
var customEnumerator = new BookmarkEnumerator(bookmarkEnumerator);
var nextMatch = finder.NextMatch(customEnumerator);
if (nextMatch == null || customMatches.ContainsKey(customEnumerator.Current))
{
continue;
}
customMatches.Add(customEnumerator.Current, nextMatch);
}
do
{
bookmarkEnumerator.MoveNext();
FindMatch findMatch;
if (customMatches.TryGetValue(bookmarkEnumerator.Current, out findMatch))
{
return(new FindResult(this, bookmarkEnumerator, findMatch));
}
findMatch = MatchInternal(bookmarkEnumerator);
if (findMatch != null)
{
return(new FindResult(this, bookmarkEnumerator, findMatch));
}
} while (!bookmarkEnumerator.AtStart);
return(null);
}
public BookmarkEnumerator(BookmarkEnumerator bookmarkEnumerator)
{
Document = bookmarkEnumerator.Document;
Start = bookmarkEnumerator.Start;
Current = bookmarkEnumerator.Current;
Forward = bookmarkEnumerator.Forward;
}
FindMatch MatchCustom(BookmarkEnumerator bookmarkEnumerator)
{
foreach (var finder in FindOptions.CustomFinders)
{
var findMatch = finder.Match(bookmarkEnumerator);
if (findMatch != null)
{
return(findMatch);
}
}
return(null);
}
public virtual FindMatch NextMatch(BookmarkEnumerator bookmarkEnumerator)
{
do
{
bookmarkEnumerator.MoveNext();
var findMatch = Match(bookmarkEnumerator);
if (findMatch != null)
{
return(findMatch);
}
} while (!bookmarkEnumerator.AtStart);
return(null);
}
public override FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
var transitionChromInfo = bookmarkEnumerator.CurrentChromInfo as TransitionChromInfo;
if (transitionChromInfo == null)
{
return(null);
}
if (transitionChromInfo.IsEmpty)
{
return(new FindMatch(Resources.UnintegratedTransitionFinder_Match_Unintegrated_transition));
}
return(null);
}
public IEnumerable <FindResult> FindAll(ILongWaitBroker longWaitBroker, SrmDocument document)
{
longWaitBroker.Message = Resources.FindPredicate_FindAll_Found_0_matches;
var customMatches = new HashSet <Bookmark> [FindOptions.CustomFinders.Count];
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
var customFinder = FindOptions.CustomFinders[iFinder];
var bookmarkSet = new HashSet <Bookmark>();
longWaitBroker.Message = string.Format(Resources.FindPredicate_FindAll_Searching_for__0__, customFinder.DisplayName);
foreach (var bookmark in customFinder.FindAll(document))
{
if (longWaitBroker.IsCanceled)
{
yield break;
}
bookmarkSet.Add(bookmark);
}
customMatches[iFinder] = bookmarkSet;
}
var bookmarkEnumerator = new BookmarkEnumerator(document);
int matchCount = 0;
do
{
bookmarkEnumerator.MoveNext();
if (longWaitBroker.IsCanceled)
{
yield break;
}
FindMatch findMatch = null;
for (int iFinder = 0; iFinder < FindOptions.CustomFinders.Count; iFinder++)
{
if (customMatches[iFinder].Contains(bookmarkEnumerator.Current))
{
findMatch = FindOptions.CustomFinders[iFinder].Match(bookmarkEnumerator);
}
}
findMatch = findMatch ?? MatchInternal(bookmarkEnumerator);
if (findMatch != null)
{
matchCount++;
longWaitBroker.Message = matchCount == 1
? Resources.FindPredicate_FindAll_Found_1_match
: string.Format(Resources.FindPredicate_FindAll_Found__0__matches, matchCount);
yield return(new FindResult(this, bookmarkEnumerator, findMatch));
}
} while (!bookmarkEnumerator.AtStart);
}
public IEnumerator <Bookmark> GetEnumerator()
{
var enumerator = new BookmarkEnumerator(this);
while (true)
{
enumerator.MoveNext();
yield return(enumerator.Current);
if (enumerator.AtStart)
{
break;
}
}
}
public override FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
var transitionChromInfo = bookmarkEnumerator.CurrentChromInfo as TransitionChromInfo;
if (transitionChromInfo == null)
{
return(null);
}
bool integrateAll = bookmarkEnumerator.Document.Settings.TransitionSettings.Integration.IsIntegrateAll;
if (!transitionChromInfo.IsGoodPeak(integrateAll))
{
return(new FindMatch(Resources.UnintegratedTransitionFinder_Match_Unintegrated_transition));
}
return(null);
}
public FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
var transitionGroupChromInfo = bookmarkEnumerator.CurrentChromInfo as TransitionGroupChromInfo;
if (transitionGroupChromInfo != null)
{
return(MatchTransitionGroup(transitionGroupChromInfo));
}
var transitionChromInfo = bookmarkEnumerator.CurrentChromInfo as TransitionChromInfo;
if (transitionChromInfo != null)
{
return(MatchTransition(transitionChromInfo));
}
return(null);
}
public virtual IEnumerable <Bookmark> FindAll(SrmDocument document)
{
var bookmarkEnumerator = new BookmarkEnumerator(document);
while (true)
{
bookmarkEnumerator.MoveNext();
if (Match(bookmarkEnumerator) != null)
{
yield return(bookmarkEnumerator.Current);
}
if (bookmarkEnumerator.AtStart)
{
yield break;
}
}
}
private FindMatch MatchInternal(BookmarkEnumerator bookmarkEnumerator)
{
if (string.IsNullOrEmpty(FindOptions.Text))
{
return(null);
}
var chromInfo = bookmarkEnumerator.CurrentChromInfo;
if (chromInfo != null)
{
return(MatchAnnotations(GetAnnotations(chromInfo)));
}
var docNode = bookmarkEnumerator.CurrentDocNode;
if (docNode == null)
{
return(null);
}
return(MatchText(docNode.GetDisplayText(DisplaySettings))
?? MatchAnnotations(docNode.Annotations));
}
public override FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
var nodePep = bookmarkEnumerator.CurrentDocNode as PeptideDocNode;
if (nodePep == null)
{
return(null);
}
if (bookmarkEnumerator.CurrentChromInfo == null)
{
_isLastNodeMatch = IsMatch(nodePep);
if (_isLastNodeMatch)
{
return(new FindMatch(string.Format(Resources.MissingScoresFinder_Match__0__missing_from_peptide, _calculatorName)));
}
}
else if (IsMatch(bookmarkEnumerator.CurrentChromInfo, nodePep) && !_isLastNodeMatch)
{
return(new FindMatch(string.Format(Resources.MissingScoresFinder_Match__0__missing_from_chromatogram_peak, _calculatorName)));
}
return(null);
}
public FindMatch NextMatch(BookmarkEnumerator bookmarkEnumerator)
{
var allBookmarks = new HashSet <Bookmark>(FindAll(bookmarkEnumerator.Document));
if (allBookmarks.Count == 0)
{
return(null);
}
do
{
bookmarkEnumerator.MoveNext();
if (allBookmarks.Contains(bookmarkEnumerator.Current))
{
var findMatch = Match(bookmarkEnumerator);
if (findMatch != null)
{
return(findMatch);
}
}
} while (!bookmarkEnumerator.AtStart);
return(null);
}
public FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
return(MatchCustom(bookmarkEnumerator) ?? MatchInternal(bookmarkEnumerator));
}
public abstract FindMatch Match(BookmarkEnumerator bookmarkEnumerator);
