public double[] GetRetentionTimes(MsDataFileUri filePath, string peptideSequence, ExplicitMods explicitMods,
RetentionTimeAlignmentIndex alignmentIndex = null)
{
string basename = filePath.GetFileNameWithoutExtension();
var source = DocumentRetentionTimes.RetentionTimeSources.Find(basename);
if (source == null)
{
return new double[0];
}
var library = PeptideSettings.Libraries.GetLibrary(source.Library);
if (library == null)
{
return new double[0];
}
var modifiedSequences = GetTypedSequences(peptideSequence, explicitMods)
.Select(typedSequence => typedSequence.ModifiedSequence);
int? index = (alignmentIndex != null ? alignmentIndex.FileIndex : null);
var times = library.GetRetentionTimesWithSequences(source.Name, modifiedSequences, ref index).ToArray();
if (alignmentIndex != null)
alignmentIndex.FileIndex = index;
return times;
}
public double[] GetRetentionTimes(string filePath, string peptideSequence, ExplicitMods explicitMods,
RetentionTimeAlignmentIndex alignmentIndex = null)
{
return GetRetentionTimes(MsDataFileUri.Parse(filePath), peptideSequence, explicitMods, alignmentIndex);
}
