private double? PredictRetentionTimeUsingSpecifiedReplicates(SrmDocument document,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
int? replicateNum,
ExportSchedulingAlgorithm algorithm,
bool singleWindow,
Predicate<ChromatogramSet> replicateFilter,
out double windowRT)
{
// If peptide has an explicitly set RT, use that
if (nodePep.ExplicitRetentionTime != null &&
(MeasuredRTWindow.HasValue || nodePep.ExplicitRetentionTime.RetentionTimeWindow.HasValue))
{
// If peptide has an explicitly set RT window, use that, or the global setting
windowRT = nodePep.ExplicitRetentionTime.RetentionTimeWindow ?? MeasuredRTWindow.Value;
return nodePep.ExplicitRetentionTime.RetentionTime;
}
// Safe defaults
double? predictedRT = null;
windowRT = 0;
// Use measurements, if set and available
bool useMeasured = (UseMeasuredRTs && MeasuredRTWindow.HasValue && document.Settings.HasResults);
if (useMeasured)
{
var schedulingGroups = GetSchedulingGroups(nodePep, nodeGroup);
var peakTime = TransitionGroupDocNode.GetSchedulingPeakTimes(schedulingGroups, document, algorithm, replicateNum, replicateFilter);
if (peakTime != null)
predictedRT = peakTime.CenterTime;
if (predictedRT.HasValue)
windowRT = MeasuredRTWindow.Value;
else if (nodePep.Children.Count > 1)
{
// If their are other children of this peptide, look for one
// with results that can be used to predict the retention time.
foreach (TransitionGroupDocNode nodeGroupOther in nodePep.Children)
{
if (!ReferenceEquals(nodeGroup, nodeGroupOther))
{
peakTime = nodeGroupOther.GetSchedulingPeakTimes(document, algorithm, replicateNum, replicateFilter);
if (peakTime != null)
predictedRT = peakTime.CenterTime;
if (predictedRT.HasValue)
{
windowRT = MeasuredRTWindow.Value;
break;
}
}
}
}
}
// If no retention time yet, and there is a predictor, use the predictor
if (!predictedRT.HasValue && RetentionTime != null && RetentionTime.IsUsable)
{
// but only if not using measured results, or the instrument supports
// variable scheduling windows
if (!useMeasured || !singleWindow || MeasuredRTWindow == RetentionTime.TimeWindow)
{
string modifiedSequence = document.Settings.GetSourceTextId(nodePep);
if (null != replicateFilter && document.Settings.HasResults)
{
var retentionTimes = new List<double>();
foreach (var chromSet in document.Settings.MeasuredResults.Chromatograms)
{
if (!replicateFilter(chromSet))
{
continue;
}
foreach (ChromFileInfo chromFileInfo in chromSet.MSDataFileInfos)
{
var conversion = RetentionTime.GetConversion(chromFileInfo.FileId);
if (null == conversion)
{
continue;
}
double? time = RetentionTime.GetRetentionTime(modifiedSequence, conversion);
if (time.HasValue)
{
retentionTimes.Add(time.Value);
}
}
}
if (retentionTimes.Count > 0)
{
predictedRT = retentionTimes.Average();
}
}
if (!predictedRT.HasValue)
{
predictedRT = RetentionTime.GetRetentionTime(modifiedSequence);
}
windowRT = RetentionTime.TimeWindow;
}
}
return predictedRT;
}
public double? PredictRetentionTime(SrmDocument document,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
int? replicateNum,
ExportSchedulingAlgorithm algorithm,
bool singleWindow,
out double windowRT)
{
return PredictRetentionTimeUsingSpecifiedReplicates(document, nodePep, nodeGroup, replicateNum, algorithm,
singleWindow, null, out windowRT);
}
