/// <summary>
/// Gets possible values for an annotation.
/// </summary>
public static IEnumerable <object> GetPossibleAnnotations(SrmDocument document, ReplicateValue replicateValue)
{
if (!document.Settings.HasResults || null == replicateValue)
{
return(new object[0]);
}
var annotationCalculator = new AnnotationCalculator(document);
return(document.Settings.MeasuredResults.Chromatograms
.Select(chromSet => replicateValue.GetValue(annotationCalculator, chromSet)).Distinct()
.OrderBy(x => x, CollectionUtil.ColumnValueComparer));
}
/// <summary>
/// Gets replicate indices for a specific grouping annotation and value.
/// </summary>
public static int[] GetReplicateIndices(SrmDocument document, ReplicateValue group, object groupValue)
{
var defaultResult = Enumerable.Range(0, document.Settings.MeasuredResults.Chromatograms.Count).ToArray();
if (group == null)
{
return(defaultResult);
}
var annotationCalculator = new AnnotationCalculator(document);
return(defaultResult.Where(i => Equals(groupValue,
group.GetValue(annotationCalculator, document.Settings.MeasuredResults.Chromatograms[i]))).ToArray());
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, ChromFileInfoId resultsFile, bool subsequent, ReplicateValue groupBy, object groupByValue, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out var referenceTarget, out var referenceMatchData, out var runTime);
var annotationCalculator = new AnnotationCalculator(doc);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (var i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
if (groupBy != null)
{
if (!Equals(groupByValue, groupBy.GetValue(annotationCalculator, chromSet)))
{
continue;
}
}
for (var j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (resultsFile == null || ReferenceEquals(resultsFile, fileInfo.FileId))) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
{
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return(doc);
}
