private bool TryGetRetentionTimes(int fileId, string filePath, out LibraryRetentionTimes retentionTimes)
{
if (fileId < 0)
{
retentionTimes = null;
return(false);
}
ILookup <Target, double?> timesLookup = _libraryEntries.ToLookup(
entry => entry.Key.Target,
entry =>
{
FileData fileData;
if (!entry.FileDatas.TryGetValue(fileId, out fileData))
{
return(null);
}
return(fileData.ApexTime);
});
var nonEmptyTimesDict = timesLookup
.Where(grouping => grouping.Any(value => value.HasValue))
.ToDictionary(grouping => grouping.Key, grouping => Tuple.Create(TimeSource.peak, grouping.OfType <double>().ToArray()));
retentionTimes = new LibraryRetentionTimes(filePath, nonEmptyTimesDict);
return(true);
}
public override bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
int j = _librarySourceFiles.IndexOf(info => Equals(filePath.ToString(), info.FilePath));
if (j != -1)
{
var source = _librarySourceFiles[j];
ILookup <Target, double[]> timesLookup = _libraryEntries.ToLookup(
entry => entry.Key.Target,
entry => entry.RetentionTimesByFileId.GetTimes(source.Id));
var timesDict = timesLookup.ToDictionary(
grouping => grouping.Key,
grouping =>
{
var array = grouping.SelectMany(values => values).ToArray();
Array.Sort(array);
return(array);
});
var nonEmptyTimesDict = timesDict
.Where(kvp => kvp.Value.Length > 0)
.ToDictionary(kvp => kvp.Key, kvp => new Tuple <TimeSource, double[]>(TimeSource.peak, kvp.Value));
retentionTimes = new LibraryRetentionTimes(filePath.ToString(), nonEmptyTimesDict);
return(true);
}
return(base.TryGetRetentionTimes(filePath, out retentionTimes));
}
public override bool TryGetIrts(out LibraryRetentionTimes retentionTimes)
{
if (_libraryIrts == null || !_libraryIrts.Any())
{
retentionTimes = null;
return(false);
}
var irtDictionary = new Dictionary <Target, Tuple <TimeSource, double[]> >();
foreach (var irt in _libraryIrts)
{
if (!irtDictionary.ContainsKey(irt.Sequence))
{
irtDictionary[irt.Sequence] = new Tuple <TimeSource, double[]>(irt.TimeSource, new [] { irt.Irt });
}
}
retentionTimes = new LibraryRetentionTimes(null, irtDictionary);
return(true);
}
public override bool TryGetIrts(out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return(false);
}
public override bool TryGetRetentionTimes(int fileIndex, out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return(false);
}
public override bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return(false);
}
/// <summary>
/// Returns the times at which a peptide was found in a particular file.
/// </summary>
public double[] GetRetentionTimes(LibraryRetentionTimes retentionTimes, string sequence, ExplicitMods mods)
{
return (from typedSequence in GetTypedSequences(sequence, mods)
from time in retentionTimes.GetRetentionTimes(typedSequence.ModifiedSequence)
select time)
.ToArray();
}
public override bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
return(TryGetRetentionTimes(FindFileInList(filePath, _sourceFiles), filePath.ToString(), out retentionTimes));
}
public override bool TryGetRetentionTimes(int fileId, out LibraryRetentionTimes retentionTimes)
{
return(TryGetRetentionTimes(fileId, _sourceFiles[fileId], out retentionTimes));
}
public override bool TryGetRetentionTimes(int fileIndex, out LibraryRetentionTimes retentionTimes)
{
return(TryGetRetentionTimes(MsDataFileUri.Parse(_librarySourceFiles[fileIndex].FilePath), out retentionTimes));
}
public bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
Assume.IsTrue(IsLoaded);
foreach (Library lib in _libraries)
{
// Only one of the available libraries may claim ownership of the file
// in question.
if (lib != null && lib.TryGetRetentionTimes(filePath, out retentionTimes))
return true;
}
retentionTimes = null;
return false;
}
public override bool TryGetRetentionTimes(int fileIndex, out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return false;
}
public override bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return false;
}
public override bool TryGetIrts(out LibraryRetentionTimes retentionTimes)
{
retentionTimes = null;
return false;
}
