public override FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
if (bookmarkEnumerator.CurrentChromInfo == null)
{
var nodePep = bookmarkEnumerator.CurrentDocNode as PeptideDocNode;
if (nodePep != null)
{
return(IsMatch(nodePep) ? new FindMatch(DisplayName) : null);
}
var nodeGroup = bookmarkEnumerator.CurrentDocNode as TransitionGroupDocNode;
if (nodeGroup != null)
{
var nodeParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent)
as PeptideDocNode;
return(!IsMatch(nodeParent) && IsMatch(nodeGroup) ? new FindMatch(DisplayName) : null);
}
var nodeTran = bookmarkEnumerator.CurrentDocNode as TransitionDocNode;
if (nodeTran != null)
{
var nodeGrandParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent.Parent)
as PeptideDocNode;
var nodeParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent)
as TransitionGroupDocNode;
return(!IsMatch(nodeGrandParent) && !IsMatch(nodeParent) && IsMatch(nodeParent, nodeTran) ? new FindMatch(DisplayName) : null);
}
}
return(null);
}
public void TestForwardBackward()
{
var assembly = Assembly.GetAssembly(typeof(BookmarkEnumeratorTest));
var stream = assembly.GetManifestResourceStream(
typeof(BookmarkEnumeratorTest).Namespace + ".BookmarkEnumeratorTest.sky");
Assert.IsNotNull(stream);
var document = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(stream);
Assert.IsNotNull(document);
var forwardEnumerator = new BookmarkEnumerator(document);
var backwardEnumerator = new BookmarkEnumerator(forwardEnumerator)
{
Forward = false
};
var forwardList = new List <Bookmark>(forwardEnumerator);
var backwardList = new List <Bookmark>(backwardEnumerator);
Assert.AreNotEqual(0, forwardList.Count);
Assert.AreEqual(forwardList.Count, backwardList.Count);
// The very last location is the same for both the forwards and backwards enumerators.
backwardList.Reverse(0, backwardList.Count - 1);
CollectionAssert.AreEqual(forwardList, backwardList);
var forwardSet = new HashSet <Bookmark>(forwardList);
Assert.AreEqual(forwardList.Count, forwardSet.Count);
forwardSet.UnionWith(backwardList);
Assert.AreEqual(forwardList.Count, forwardSet.Count);
}
public override FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
if (bookmarkEnumerator.CurrentChromInfo == null)
{
var nodePep = bookmarkEnumerator.CurrentDocNode as PeptideDocNode;
if (nodePep != null)
{
return IsMatch(nodePep) ? new FindMatch(DisplayName) : null;
}
var nodeGroup = bookmarkEnumerator.CurrentDocNode as TransitionGroupDocNode;
if (nodeGroup != null)
{
var nodeParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent)
as PeptideDocNode;
return !IsMatch(nodeParent) && IsMatch(nodeGroup) ? new FindMatch(DisplayName) : null;
}
var nodeTran = bookmarkEnumerator.CurrentDocNode as TransitionDocNode;
if (nodeTran != null)
{
var nodeGrandParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent.Parent)
as PeptideDocNode;
var nodeParent = bookmarkEnumerator.Document.FindNode(bookmarkEnumerator.IdentityPath.Parent)
as TransitionGroupDocNode;
return !IsMatch(nodeGrandParent) && !IsMatch(nodeParent) && IsMatch(nodeParent, nodeTran) ? new FindMatch(DisplayName) : null;
}
}
return null;
}
public FindResult(FindPredicate findPredicate, BookmarkEnumerator bookmarkEnumerator, FindMatch match)
{
FindPredicate = findPredicate;
Bookmark = bookmarkEnumerator.Current;
Document = bookmarkEnumerator.Document;
LocationName = bookmarkEnumerator.GetLocationName(findPredicate.DisplaySettings);
LocationType = bookmarkEnumerator.GetLocationType();
FindMatch = match;
IsValid = true;
}
public FindResult(FindPredicate findPredicate, BookmarkEnumerator bookmarkEnumerator, FindMatch match)
{
FindPredicate = findPredicate;
Bookmark = bookmarkEnumerator.Current;
Document = bookmarkEnumerator.Document;
LocationName = bookmarkEnumerator.GetLocationName(findPredicate.DisplaySettings);
LocationType = bookmarkEnumerator.GetLocationType();
FindMatch = match;
IsValid = true;
}
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 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)
{
if (bookmarkEnumerator.ResultsIndex == -1)
{
var pair = _pairs.Find(p => ReferenceEquals(p.Peptide, bookmarkEnumerator.CurrentDocNode));
if (pair != null)
{
var displayText = GetDisplayText(_displayCV, pair.Annotation);
return(new FindMatch(displayText));
}
}
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;
}
}
}
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 FindResult ChangeDocument(SrmDocument document)
{
var result = new FindResult(this)
{
Document = document
};
var bookMarkEnumerator = BookmarkEnumerator.TryGet(document, Bookmark);
FindMatch findMatch = null;
if (bookMarkEnumerator != null)
{
findMatch = FindPredicate.Match(bookMarkEnumerator);
}
if (findMatch == null)
{
result.IsValid = false;
}
else
{
result.IsValid = true;
result.FindMatch = findMatch;
}
return(result);
}
public void TestForwardBackward()
{
var assembly = Assembly.GetAssembly(typeof (BookmarkEnumeratorTest));
var stream = assembly.GetManifestResourceStream(
typeof (BookmarkEnumeratorTest).Namespace + ".BookmarkEnumeratorTest.sky");
Assert.IsNotNull(stream);
var document = (SrmDocument) new XmlSerializer(typeof (SrmDocument)).Deserialize(stream);
Assert.IsNotNull(document);
var forwardEnumerator = new BookmarkEnumerator(document);
var backwardEnumerator = new BookmarkEnumerator(forwardEnumerator) {Forward = false};
var forwardList = new List<Bookmark>(forwardEnumerator);
var backwardList = new List<Bookmark>(backwardEnumerator);
Assert.AreNotEqual(0, forwardList.Count);
Assert.AreEqual(forwardList.Count, backwardList.Count);
// The very last location is the same for both the forwards and backwards enumerators.
backwardList.Reverse(0, backwardList.Count - 1);
CollectionAssert.AreEqual(forwardList, backwardList);
var forwardSet = new HashSet<Bookmark>(forwardList);
Assert.AreEqual(forwardList.Count, forwardSet.Count);
forwardSet.UnionWith(backwardList);
Assert.AreEqual(forwardList.Count, forwardSet.Count);
}
public abstract FindMatch Match(BookmarkEnumerator bookmarkEnumerator);
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 FindMatch Match(BookmarkEnumerator bookmarkEnumerator)
{
return MatchCustom(bookmarkEnumerator) ?? MatchInternal(bookmarkEnumerator);
}
FindMatch MatchCustom(BookmarkEnumerator bookmarkEnumerator)
{
foreach (var finder in FindOptions.CustomFinders)
{
var findMatch = finder.Match(bookmarkEnumerator);
if (findMatch != null)
{
return findMatch;
}
}
return null;
}
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 void HighlightFindResult(FindResult findResult)
{
if (!IsComplete)
{
_pendingFindResult = findResult;
return;
}
var bookmarkEnumerator = BookmarkEnumerator.TryGet(_dataSchema.Document, findResult.Bookmark);
if (bookmarkEnumerator == null)
{
return;
}
var chromInfo = bookmarkEnumerator.CurrentChromInfo;
if (chromInfo == null)
{
return;
}
int?iRowMatch = null;
for (int iRow = 0; iRow < BindingListSource.Count; iRow++)
{
var rowItem = BindingListSource[iRow] as RowItem;
if (rowItem == null)
{
continue;
}
var replicate = rowItem.Value as Replicate;
if (replicate != null)
{
if (replicate.Files.Any(file => ReferenceEquals(file.ChromFileInfoId, chromInfo.FileId)))
{
iRowMatch = iRow;
break;
}
}
var result = rowItem.Value as Result;
if (null != result)
{
if (ReferenceEquals(result.GetResultFile().ChromFileInfoId, chromInfo.FileId))
{
iRowMatch = iRow;
break;
}
}
}
if (!iRowMatch.HasValue)
{
return;
}
BindingListSource.Position = iRowMatch.Value;
DataGridViewColumn column;
if (findResult.FindMatch.Note)
{
column = FindColumn(PropertyPath.Root.Property("Note")); // Not L10N
}
else if (findResult.FindMatch.AnnotationName != null)
{
column = FindColumn(PropertyPath.Root.Property(
AnnotationDef.ANNOTATION_PREFIX + findResult.FindMatch.AnnotationName));
}
else
{
return;
}
if (null != column && null != DataGridView.CurrentRow)
{
DataGridView.CurrentCell = DataGridView.CurrentRow.Cells[column.Index];
}
}
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);
}