public static RawTimeIntensities ReadFromStream(Stream stream)
{
var chromatogramGroupData = new ChromatogramGroupData();
chromatogramGroupData.MergeFrom(new CodedInputStream(stream));
return(FromChromatogramGroupData(chromatogramGroupData));
}
public ChromatogramGroupData ToChromatogramGroupData()
{
var timeLists = new Dictionary <ImmutableList <float>, int>();
var scanIdLists = new Dictionary <ImmutableList <int>, int>();
var chromatogramGroupData = new ChromatogramGroupData();
for (int i = 0; i < TransitionTimeIntensities.Count; i++)
{
var timeIntensities = TransitionTimeIntensities[i];
var chromatogram = new ChromatogramGroupData.Types.Chromatogram();
int timeListIndex;
if (!timeLists.TryGetValue(timeIntensities.Times, out timeListIndex))
{
timeListIndex = timeLists.Count + 1;
timeLists.Add(timeIntensities.Times, timeListIndex);
var timeList = new ChromatogramGroupData.Types.TimeList();
timeList.Times.AddRange(timeIntensities.Times);
chromatogramGroupData.TimeLists.Add(timeList);
}
chromatogram.TimeListIndex = timeListIndex;
chromatogram.Intensities.AddRange(timeIntensities.Intensities);
if (null != timeIntensities.MassErrors)
{
chromatogram.MassErrors100X.AddRange(timeIntensities.MassErrors.Select(error => (int)Math.Round(error * 100)));
}
if (null != timeIntensities.ScanIds)
{
int scanIdListIndex;
if (!scanIdLists.TryGetValue(timeIntensities.ScanIds, out scanIdListIndex))
{
scanIdListIndex = scanIdLists.Count + 1;
scanIdLists.Add(timeIntensities.ScanIds, scanIdListIndex);
var scanIdList = new ChromatogramGroupData.Types.ScanIdList();
scanIdList.ScanIds.AddRange(timeIntensities.ScanIds);
chromatogramGroupData.ScanIdLists.Add(scanIdList);
}
chromatogram.ScanIdListIndex = scanIdListIndex;
}
chromatogramGroupData.Chromatograms.Add(chromatogram);
}
if (InterpolationParams != null)
{
chromatogramGroupData.InterpolatedStartTime = InterpolationParams.StartTime;
chromatogramGroupData.InterpolatedEndTime = InterpolationParams.EndTime;
chromatogramGroupData.InterpolatedNumPoints = InterpolationParams.NumPoints;
chromatogramGroupData.InterpolatedDelta = InterpolationParams.IntervalDelta;
chromatogramGroupData.InferZeroes = InterpolationParams.InferZeroes;
}
if (TimeIntervals != null)
{
chromatogramGroupData.TimeIntervals = new ChromatogramGroupData.Types.TimeIntervals();
chromatogramGroupData.TimeIntervals.StartTimes.AddRange(TimeIntervals.Starts);
chromatogramGroupData.TimeIntervals.EndTimes.AddRange(TimeIntervals.Ends);
}
return(chromatogramGroupData);
}
public static RawTimeIntensities FromChromatogramGroupData(ChromatogramGroupData chromatogramGroupData)
{
var timeIntensitiesList = new List <TimeIntensities>();
var timeLists = chromatogramGroupData.TimeLists.Select(timeList => ImmutableList.ValueOf(timeList.Times)).ToArray();
var scanIdLists = chromatogramGroupData.ScanIdLists
.Select(scanIdList => ImmutableList.ValueOf(scanIdList.ScanIds)).ToArray();
foreach (var chromatogram in chromatogramGroupData.Chromatograms)
{
IEnumerable <float> massErrors = null;
if (chromatogram.MassErrors100X.Count > 0)
{
massErrors = chromatogram.MassErrors100X.Select(error => error / 100.0f);
}
else if (chromatogram.MassErrorsDeprecated.Count > 0)
{
massErrors = chromatogram.MassErrorsDeprecated;
}
var timeIntensities = new TimeIntensities(timeLists[chromatogram.TimeListIndex - 1],
chromatogram.Intensities,
massErrors,
chromatogram.ScanIdListIndex == 0 ? null : scanIdLists[chromatogram.ScanIdListIndex - 1]);
timeIntensitiesList.Add(timeIntensities);
}
InterpolationParams interpolationParams;
if (chromatogramGroupData.InterpolatedNumPoints == 0)
{
interpolationParams = null;
}
else
{
interpolationParams = new InterpolationParams(chromatogramGroupData.InterpolatedStartTime, chromatogramGroupData.InterpolatedEndTime, chromatogramGroupData.InterpolatedNumPoints, chromatogramGroupData.InterpolatedDelta)
.ChangeInferZeroes(chromatogramGroupData.InferZeroes);
}
var rawTimeIntensities = new RawTimeIntensities(timeIntensitiesList, interpolationParams);
if (chromatogramGroupData.TimeIntervals != null)
{
var startTimes = chromatogramGroupData.TimeIntervals.StartTimes;
var endTimes = chromatogramGroupData.TimeIntervals.EndTimes;
var timeIntervals = TimeIntervals.FromIntervals(Enumerable.Range(0, startTimes.Count)
.Select(i => new KeyValuePair <float, float>(startTimes[i], endTimes[i])));
rawTimeIntensities = rawTimeIntensities.ChangeTimeIntervals(timeIntervals);
}
return(rawTimeIntensities);
}
