public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int? resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(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;
}
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);
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int?resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(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);
}
