private void AddChromInfo(ChromInfoList <TransitionGroupChromInfo> chromGroupInfos, ChromInfoList <TransitionChromInfo> chromInfos,
Dictionary <int, int> dictPpmBin2ToCount, List <double> vals)
{
if (chromInfos.IsEmpty || chromGroupInfos.IsEmpty)
{
return;
}
foreach (var chromInfo in chromInfos)
{
if (_transition == TransitionMassError.best && chromInfo.RankByLevel != 1)
{
continue;
}
if (_pointsType == PointsTypeMassError.targets_1FDR && chromInfo.GetMatchingQValue(chromGroupInfos) > 0.01)
{
continue;
}
var massError = chromInfo.MassError;
if (massError.HasValue)
{
vals.Add((float)massError);
var ppmBin2 = (int)Math.Floor(massError.Value / _binSize);
if (dictPpmBin2ToCount.ContainsKey(ppmBin2))
{
dictPpmBin2ToCount[ppmBin2]++;
}
else
{
dictPpmBin2ToCount.Add(ppmBin2, 1);
}
}
}
}
private Results <TransitionChromInfo> MergeResultsUserInfo(
SrmSettings settings, Results <TransitionChromInfo> results)
{
if (!HasResults)
{
return(Results);
}
var dictFileIdToChromInfo = results.SelectMany(l => l)
// Merge everything that does not already exist (handled below),
// as merging only user modified causes loss of information in
// updates
//.Where(i => i.IsUserModified)
.ToDictionary(i => i.FileIndex);
var listResults = new List <ChromInfoList <TransitionChromInfo> >();
for (int i = 0; i < results.Count; i++)
{
List <TransitionChromInfo> listChromInfo = null;
var chromSet = settings.MeasuredResults.Chromatograms[i];
var chromInfoList = Results[i];
foreach (var fileInfo in chromSet.MSDataFileInfos)
{
TransitionChromInfo chromInfo;
if (!dictFileIdToChromInfo.TryGetValue(fileInfo.FileIndex, out chromInfo))
{
continue;
}
if (listChromInfo == null)
{
listChromInfo = new List <TransitionChromInfo>(chromInfoList);
}
int iExist = listChromInfo.IndexOf(chromInfoExist =>
ReferenceEquals(chromInfoExist.FileId, chromInfo.FileId) &&
chromInfoExist.OptimizationStep == chromInfo.OptimizationStep);
if (iExist == -1)
{
listChromInfo.Add(chromInfo);
}
else if (chromInfo.IsUserModified)
{
listChromInfo[iExist] = chromInfo;
}
}
if (listChromInfo != null)
{
chromInfoList = new ChromInfoList <TransitionChromInfo>(listChromInfo);
}
listResults.Add(chromInfoList);
}
if (ArrayUtil.InnerReferencesEqual <TransitionChromInfo, ChromInfoList <TransitionChromInfo> >(listResults, Results))
{
return(Results);
}
return(new Results <TransitionChromInfo>(listResults));
}
private void AddChromInfo(ChromInfoList <TransitionGroupChromInfo> chromGroupInfos, ChromInfoList <TransitionChromInfo> chromInfos,
double mz, int[,] counts2D)
{
if (chromInfos.IsEmpty)
{
return;
}
foreach (var chromInfo in chromInfos)
{
if (_transition == TransitionMassError.best && chromInfo.RankByLevel != 1)
{
continue;
}
if (_pointsType == PointsTypeMassError.targets_1FDR && chromInfo.GetMatchingQValue(chromGroupInfos) > 0.01)
{
continue;
}
var massError = chromInfo.MassError;
if (massError.HasValue)
{
var xVal = _xAxis == Histogram2DXAxis.mass_to_charge ? mz : chromInfo.RetentionTime;
if (ReferenceEquals(counts2D, EMPTY_COUNTS))
{
_maxMass = Math.Max(_maxMass, massError.Value);
_minMass = Math.Min(_minMass, massError.Value);
_maxX = Math.Max(_maxX, xVal);
_minX = Math.Min(_minX, xVal);
}
else
{
int x = (int)Math.Floor((xVal - _minX) / ((_maxX - _minX) / xAxisBins));
int y = (int)Math.Floor((massError.Value - _minMass) / _binSizePpm);
counts2D[Math.Min(x, counts2D.GetLength(0) - 1), Math.Min(y, counts2D.GetLength(1) - 1)]++;
}
}
}
}
private IDictionary <MsDataFileUri, TransitionChromInfo> ToDict(SrmDocument doc, ChromInfoList <TransitionChromInfo> chromInfoList)
{
return(chromInfoList.ToDictionary(c =>
doc.MeasuredResults.MSDataFileInfos.First(fi => ReferenceEquals(fi.FileId, c.FileId)).FilePath));
}
private double GetHeight(ChromInfoList <TransitionGroupChromInfo> transitionGroupChromInfos)
{
return(!transitionGroupChromInfos.IsEmpty ? transitionGroupChromInfos.Max(c => c.Height ?? 0) : 0);
}
public SrmDocument AddAnnotationTestValues(SrmDocument document)
{
_counter = 0;
_elementCount = 0;
document = document.ChangeSettings(document.Settings.ChangeDataSettings(
document.Settings.DataSettings.ChangeAnnotationDefs(ImmutableList.ValueOf(GetTestAnnotations()))));
var measuredResults = document.MeasuredResults;
if (measuredResults != null)
{
var chromatograms = measuredResults.Chromatograms.ToArray();
for (int i = 0; i < chromatograms.Length; i++)
{
_elementCount++;
chromatograms[i] = chromatograms[i].ChangeAnnotations(
AddAnnotations(chromatograms[i].Annotations, AnnotationDef.AnnotationTarget.replicate));
}
document = document.ChangeMeasuredResults(measuredResults.ChangeChromatograms(chromatograms));
}
var proteins = document.MoleculeGroups.ToArray();
for (int iProtein = 0; iProtein < proteins.Length; iProtein++)
{
var protein = proteins[iProtein];
_elementCount++;
protein = (PeptideGroupDocNode)protein.ChangeAnnotations(AddAnnotations(protein.Annotations,
AnnotationDef.AnnotationTarget.protein));
var peptides = protein.Molecules.ToArray();
for (int iPeptide = 0; iPeptide < peptides.Length; iPeptide++)
{
var peptide = peptides[iPeptide];
_elementCount++;
peptide = (PeptideDocNode)peptide.ChangeAnnotations(AddAnnotations(peptide.Annotations,
AnnotationDef.AnnotationTarget.peptide));
var precursors = peptide.TransitionGroups.ToArray();
for (int iPrecursor = 0; iPrecursor < precursors.Length; iPrecursor++)
{
var precursor = precursors[iPrecursor];
precursor = (TransitionGroupDocNode)precursor.ChangeAnnotations(
AddAnnotations(precursor.Annotations,
AnnotationDef.AnnotationTarget.precursor));
_elementCount++;
var transitions = precursor.Transitions.ToArray();
for (int iTransition = 0; iTransition < transitions.Length; iTransition++)
{
var transition = transitions[iTransition];
_elementCount++;
transition = (TransitionDocNode)transition.ChangeAnnotations(
AddAnnotations(transition.Annotations,
AnnotationDef.AnnotationTarget.transition));
if (transition.Results != null)
{
var results = transition.Results.ToArray();
for (int replicateIndex = 0; replicateIndex < results.Length; replicateIndex++)
{
_elementCount += results[replicateIndex].Count;
results[replicateIndex] = new ChromInfoList <TransitionChromInfo>(
results[replicateIndex]
.Select(chromInfo => chromInfo.ChangeAnnotations(AddAnnotations(
chromInfo.Annotations,
AnnotationDef.AnnotationTarget.transition_result))));
}
transition = transition.ChangeResults(new Results <TransitionChromInfo>(results));
}
transitions[iTransition] = transition;
}
if (precursor.Results != null)
{
var results = precursor.Results.ToArray();
for (int replicateIndex = 0; replicateIndex < results.Length; replicateIndex++)
{
_elementCount += results[replicateIndex].Count;
results[replicateIndex] = new ChromInfoList <TransitionGroupChromInfo>(
results[replicateIndex].Select(chromInfo =>
chromInfo.ChangeAnnotations(AddAnnotations(chromInfo.Annotations,
AnnotationDef.AnnotationTarget.precursor_result))));
}
precursor = precursor.ChangeResults(new Results <TransitionGroupChromInfo>(results));
}
precursor = (TransitionGroupDocNode)precursor.ChangeChildren(transitions);
precursors[iPrecursor] = precursor;
}
peptide = (PeptideDocNode)peptide.ChangeChildren(precursors);
peptides[iPeptide] = peptide;
}
protein = (PeptideGroupDocNode)protein.ChangeChildren(peptides);
proteins[iProtein] = protein;
}
return((SrmDocument)document.ChangeChildren(proteins));
}
private double GetHeight(ChromInfoList<TransitionGroupChromInfo> transitionGroupChromInfos)
{
return transitionGroupChromInfos != null ? transitionGroupChromInfos.Max(c => c.Height ?? 0) : 0;
}
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 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));
}
