Fix AssumptionException in PeakMatcher.cs (#3190)

Fixed error doing "Apply peak to all" when a particular replicate has no chromatograms that match transitions in the document but does have some hidden MS1 chromatograms (reported by Jeannie)

pwiz_tools/Skyline/Model/PeakMatcher.cs

@@ -61,6 +61,8 @@ private static void GetReferenceData(SrmDocument doc, PeptideDocNode nodePep, Tr
  var chromGroupInfo = chromGroupInfos.FirstOrDefault(info => Equals(chromSet.GetFileInfo(tranGroupChromInfo.FileId).FilePath, info.FilePath));
  if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.TimeIntensitiesGroup.HasAnyPoints)
  return;
+ if (!GetTransitionChromatogramInfos(nodeTranGroup, chromGroupInfo, mzMatchTolerance).Any())
+ return;
 
  runTime = chromGroupInfo.RunStartTime;
 
@@ -221,6 +223,8 @@ private static PeakMatch GetPeakMatch(SrmDocument doc, ChromatogramSet chromSet,
  var chromGroupInfo = loadInfos.FirstOrDefault(info => Equals(info.FilePath, fileInfo.FilePath));
  if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.TimeIntensitiesGroup.HasAnyPoints)
  return null;
+ if (!GetTransitionChromatogramInfos(nodeTranGroup, chromGroupInfo, mzMatchTolerance).Any())
+ return null;
 
  var matchData = new List<PeakMatchData>();
  double totalArea = chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area));
@@ -306,18 +310,23 @@ private static PeakMatch GetPeakMatch(SrmDocument doc, ChromatogramSet chromSet,
  ChromatogramGroupInfo chromGroupInfo, int peakIndex, float mzMatchTolerance)
  {
  ChromPeak? largestPeak = null;
- foreach (var peak in
- from transitionDocNode in nodeTranGroup.Transitions
- select chromGroupInfo.GetTransitionInfo(transitionDocNode, mzMatchTolerance)
- into chromInfo where chromInfo != null
- select chromInfo.GetPeak(peakIndex))
+ foreach (var peak in GetTransitionChromatogramInfos(nodeTranGroup, chromGroupInfo, mzMatchTolerance)
+ .Select(chromInfo => chromInfo.GetPeak(peakIndex)))
  {
  if (largestPeak == null || peak.Height > largestPeak.Value.Height)
  largestPeak = peak;
  }
  return largestPeak;
  }
 
+ private static IEnumerable<ChromatogramInfo> GetTransitionChromatogramInfos(TransitionGroupDocNode nodeTranGroup,
+ ChromatogramGroupInfo chromGroupInfo, float mzMatchTolerance)
+ {
+ return nodeTranGroup.Transitions
+ .Select(transition => chromGroupInfo.GetTransitionInfo(transition, mzMatchTolerance))
+ .Where(chromatogramInfo => chromatogramInfo != null);
+ }
+
  private static PeakMatch MakePeakMatchBetween(float scale, PeakMatchData referenceTarget, PeakAlignment prev, PeakAlignment next)
  {
  if (prev == null && next == null)