private Annotations GetResultAnnotations(SrmDocument document, ResultRef resultRef)
{
var measuredResults = document.MeasuredResults;
if (measuredResults == null)
{
throw ElementNotFoundException(resultRef);
}
var nodeRef = (NodeRef)resultRef.Parent;
var identityPath = ToIdentityPath(nodeRef);
var docNode = document.FindNode(identityPath);
for (int replicateIndex = 0; replicateIndex < measuredResults.Chromatograms.Count; replicateIndex++)
{
var chromSet = measuredResults.Chromatograms[replicateIndex];
if (resultRef.Matches(chromSet))
{
var transitionGroup = docNode as TransitionGroupDocNode;
if (transitionGroup != null)
{
if (transitionGroup.Results == null || transitionGroup.Results.Count <= replicateIndex)
{
throw ElementNotFoundException(resultRef);
}
int i = IndexOfChromInfo(chromSet, (PrecursorResultRef)resultRef,
transitionGroup.Results[replicateIndex]);
if (i < 0)
{
throw ElementNotFoundException(resultRef);
}
return(transitionGroup.Results[replicateIndex][i].Annotations);
}
else
{
var transition = docNode as TransitionDocNode;
if (transition != null)
{
if (transition.Results == null || transition.Results.Count <= replicateIndex)
{
throw ElementNotFoundException(resultRef);
}
int i = IndexOfChromInfo(chromSet, (TransitionResultRef)resultRef,
transition.Results[replicateIndex]);
if (i < 0)
{
throw ElementNotFoundException(resultRef);
}
return(transition.Results[replicateIndex][i].Annotations);
}
else
{
throw AnnotationsNotSupported(resultRef);
}
}
}
}
throw ElementNotFoundException(resultRef);
}
public SrmDocument SetResultAnnotations(SrmDocument document, ResultRef resultRef, Annotations annotations)
{
var measuredResults = document.MeasuredResults;
if (measuredResults == null)
{
throw ElementNotFoundException(resultRef);
}
var nodeRef = (NodeRef)resultRef.Parent;
var identityPath = ToIdentityPath(nodeRef);
var docNode = document.FindNode(identityPath);
for (int replicateIndex = 0; replicateIndex < measuredResults.Chromatograms.Count; replicateIndex++)
{
var chromSet = measuredResults.Chromatograms[replicateIndex];
if (resultRef.Matches(chromSet))
{
var transitionGroup = docNode as TransitionGroupDocNode;
if (transitionGroup != null)
{
var results = transitionGroup.Results.ToArray();
results[replicateIndex] = SetChromInfoAnnotations(chromSet, (PrecursorResultRef)resultRef,
results[replicateIndex], annotations);
docNode = ((TransitionGroupDocNode)docNode).ChangeResults(
new Results <TransitionGroupChromInfo>(results));
}
else
{
var transition = docNode as TransitionDocNode;
if (transition != null)
{
var results = transition.Results.ToArray();
results[replicateIndex] = SetChromInfoAnnotations(chromSet, (TransitionResultRef)resultRef,
results[replicateIndex], annotations);
docNode = ((TransitionDocNode)docNode).ChangeResults(
new Results <TransitionChromInfo>(results));
}
else
{
throw AnnotationsNotSupported(resultRef);
}
}
return((SrmDocument)document.ReplaceChild(identityPath.Parent, docNode));
}
}
throw ElementNotFoundException(resultRef);
}
private int IndexOfChromInfo <TDocNode, TChromInfo>(ChromatogramSet chromatogramSet,
ResultRef <TDocNode, TChromInfo> resultRef, ChromInfoList <TChromInfo> chromInfoList)
where TDocNode : DocNode where TChromInfo : ChromInfo
{
var chromFileInfo = resultRef.FindChromFileInfo(chromatogramSet);
for (int i = 0; i < chromInfoList.Count; i++)
{
var chromInfo = chromInfoList[i];
if (!ReferenceEquals(chromInfo.FileId, chromFileInfo.Id))
{
continue;
}
if (resultRef.GetOptimizationStep(chromInfo) != resultRef.OptimizationStep)
{
continue;
}
return(i);
}
return(-1);
}
private IEnumerable <Tuple <ElementRef, Annotations> > GetNodeResultAnnotations <TDocNode, TChromInfo>(
ResultRef <TDocNode, TChromInfo> resultRef,
Results <TChromInfo> results) where TDocNode : DocNode where TChromInfo : ChromInfo
{
if (null == results)
{
yield break;
}
for (int i = 0; i < results.Count; i++)
{
var chromatogramSet = Document.Settings.MeasuredResults.Chromatograms[i];
foreach (var chromInfo in results[i])
{
if (resultRef.GetOptimizationStep(chromInfo) != 0)
{
continue;
}
yield return(Tuple.Create((ElementRef)resultRef.ChangeChromInfo(chromatogramSet, chromInfo), resultRef.GetAnnotations(chromInfo)));
}
}
}
protected bool Equals(ResultRef other)
{
return(base.Equals(other) && OptimizationStep == other.OptimizationStep && string.Equals(ResultFileName, other.ResultFileName) && Equals(ResultFilePath, other.ResultFilePath));
}
private ChromInfoList <TChromInfo> SetChromInfoAnnotations <TDocNode, TChromInfo>(ChromatogramSet chromatogramSet,
ResultRef <TDocNode, TChromInfo> resultRef, ChromInfoList <TChromInfo> chromInfoList,
Annotations annotations) where TDocNode : DocNode where TChromInfo : ChromInfo
{
int i = IndexOfChromInfo(chromatogramSet, resultRef, chromInfoList);
if (i < 0)
{
throw ElementNotFoundException(resultRef);
}
var newChromInfoList = chromInfoList.ToArray();
newChromInfoList[i] = resultRef.ChangeAnnotations(newChromInfoList[i], annotations);
return(new ChromInfoList <TChromInfo>(newChromInfoList));
}
