public static MinimizedChromGroup Discard(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
return(new MinimizedChromGroup(chromGroupHeaderInfo)
{
RetainedTransitionIndexes = new int[0]
});
}
public static void MakeChromatogramInfo(double precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = new CrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, chromGroup.Times, chromData.Intensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak, new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo5(new ChromGroupHeaderInfo(
(float)precursorMz, 0, 1, 0, peaks.Length, 0, 0,
chromGroup.Times.Length, 0, 0));
chromatogramInfo = new ChromatogramInfo(header,
new Dictionary <Type, int>(), 0,
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, 0, 0, ChromSource.unknown), },
peaks, null,
chromGroup.Times, new[] { chromData.Intensities }, null, null);
}
public void WriteChromGroup(ChromatogramGroupInfo originalChromGroup, MinimizedChromGroup minimizedChromGroup)
{
if (minimizedChromGroup.RetainedTransitionIndexes.Count == 0)
{
return;
}
var originalHeader = originalChromGroup.Header;
int fileIndex = originalHeader.FileIndex;
int startTransitionIndex = _transitions.Count;
int startPeakIndex = _peakCount;
int startScoreIndex = _scoreCount;
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
int iScores = originalHeader.StartScoreIndex + iPeak*_scoreTypes.Count;
var scores = _originalCache.GetCachedScores(iScores).ToArray();
PrimitiveArrays.Write(_outputStreamScores, scores);
_scoreCount += scores.Length;
}
int numPoints = minimizedChromGroup.OptimizedLastScan - minimizedChromGroup.OptimizedFirstScan + 1;
var retainedPeakIndexes = new HashSet<int>();
if (minimizedChromGroup.OptimizedStartTime.HasValue && minimizedChromGroup.OptimizedEndTime.HasValue)
{
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
bool outsideRange = false;
for (var transitionIndex = 0; transitionIndex < originalHeader.NumTransitions; transitionIndex++)
{
if (!minimizedChromGroup.RetainedTransitionIndexes.Contains(transitionIndex))
continue;
var peak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
transitionIndex*originalHeader.NumPeaks + iPeak);
if (peak.StartTime < minimizedChromGroup.OptimizedStartTime.Value ||
peak.EndTime > minimizedChromGroup.OptimizedEndTime.Value)
{
outsideRange = true;
break;
}
}
if (!outsideRange)
{
retainedPeakIndexes.Add(iPeak);
}
}
}
else
{
retainedPeakIndexes.UnionWith(Enumerable.Range(0, originalHeader.NumPeaks));
}
int numPeaks = retainedPeakIndexes.Count;
int maxPeakIndex;
if (retainedPeakIndexes.Contains(originalHeader.MaxPeakIndex))
{
maxPeakIndex = retainedPeakIndexes.Count(index => index < originalHeader.MaxPeakIndex);
}
else
{
maxPeakIndex = -1;
}
long location = _outputStream.Position;
float[] times = originalChromGroup.Times.Skip(minimizedChromGroup.OptimizedFirstScan).Take(numPoints).ToArray();
List<float[]> intensities = new List<float[]>();
List<short[]> massError10Xs = originalChromGroup.MassError10XArray != null
? new List<short[]>()
: null;
int[][] scanIndexes = null;
if (originalChromGroup.ScanIndexes != null)
{
scanIndexes = new int[originalChromGroup.ScanIndexes.Length][];
for (int i = 0; i < scanIndexes.Length; i++)
{
if (originalChromGroup.ScanIndexes[i] != null)
{
scanIndexes[i] =
originalChromGroup.ScanIndexes[i].Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints)
.ToArray();
}
}
}
foreach (var originalIndex in minimizedChromGroup.RetainedTransitionIndexes)
{
_transitions.Add(_originalCache.GetTransition(originalIndex + originalHeader.StartTransitionIndex));
for (int originalPeakIndex = 0; originalPeakIndex < originalHeader.NumPeaks; originalPeakIndex++)
{
if (!retainedPeakIndexes.Contains(originalPeakIndex))
continue;
var originalPeak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
originalIndex*originalHeader.NumPeaks +
originalPeakIndex);
_peakCount++;
ChromPeak.WriteArray(_outputStreamPeaks.SafeFileHandle, new[] {originalPeak});
}
intensities.Add(originalChromGroup.IntensityArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
if (massError10Xs != null)
{
massError10Xs.Add(originalChromGroup.MassError10XArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
}
}
var massError10XArray = massError10Xs != null ? massError10Xs.ToArray() : null;
byte[] points = ChromatogramCache.TimeIntensitiesToBytes(times, intensities.ToArray(), massError10XArray, scanIndexes);
// Compress the data (can be huge for AB data with lots of zeros)
byte[] pointsCompressed = points.Compress(3);
int lenCompressed = pointsCompressed.Length;
_outputStream.Write(pointsCompressed, 0, lenCompressed);
var header = new ChromGroupHeaderInfo5(originalHeader.Precursor,
originalHeader.TextIdIndex,
originalHeader.TextIdLen,
fileIndex,
_transitions.Count - startTransitionIndex,
startTransitionIndex,
numPeaks,
startPeakIndex,
startScoreIndex,
maxPeakIndex,
numPoints,
pointsCompressed.Length,
location,
originalHeader.Flags,
originalHeader.StatusId,
originalHeader.StatusRank);
_chromGroupHeaderInfos.Add(header);
}
private static long GetFileSize(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
return CHROM_GROUP_HEADER_INFO_SIZE + chromGroupHeaderInfo.CompressedSize
+ chromGroupHeaderInfo.NumPeaks * chromGroupHeaderInfo.NumTransitions * PEAK_SIZE
+ chromGroupHeaderInfo.NumTransitions * TRANSITION_SIZE;
}
public static MinimizedChromGroup Discard(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
return new MinimizedChromGroup(chromGroupHeaderInfo)
{
RetainedTransitionIndexes = new int[0]
};
}
public MinimizedChromGroup(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
ChromGroupHeaderInfo = chromGroupHeaderInfo;
OptimizedFirstScan = 0;
OptimizedLastScan = chromGroupHeaderInfo.NumPoints - 1;
}
private int CompareLocation(ChromGroupHeaderInfo5 chromGroupHeaderInfo1, ChromGroupHeaderInfo5 chromGroupHeaderInfo2)
{
return chromGroupHeaderInfo1.LocationPoints.CompareTo(chromGroupHeaderInfo2.LocationPoints);
}
private int CompareLocation(ChromGroupHeaderInfo5 chromGroupHeaderInfo1, ChromGroupHeaderInfo5 chromGroupHeaderInfo2)
{
return(chromGroupHeaderInfo1.LocationPoints.CompareTo(chromGroupHeaderInfo2.LocationPoints));
}
public void WriteChromGroup(ChromatogramGroupInfo originalChromGroup, MinimizedChromGroup minimizedChromGroup)
{
if (minimizedChromGroup.RetainedTransitionIndexes.Count == 0)
{
return;
}
var originalHeader = originalChromGroup.Header;
int fileIndex = originalHeader.FileIndex;
int startTransitionIndex = _transitions.Count;
int startPeakIndex = _peakCount;
int startScoreIndex = _scoreCount;
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
int iScores = originalHeader.StartScoreIndex + iPeak * _scoreTypes.Count;
var scores = _originalCache.GetCachedScores(iScores).ToArray();
PrimitiveArrays.Write(_outputStreamScores, scores);
_scoreCount += scores.Length;
}
int numPoints = minimizedChromGroup.OptimizedLastScan - minimizedChromGroup.OptimizedFirstScan + 1;
var retainedPeakIndexes = new HashSet <int>();
if (minimizedChromGroup.OptimizedStartTime.HasValue && minimizedChromGroup.OptimizedEndTime.HasValue)
{
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
bool outsideRange = false;
for (var transitionIndex = 0; transitionIndex < originalHeader.NumTransitions; transitionIndex++)
{
if (!minimizedChromGroup.RetainedTransitionIndexes.Contains(transitionIndex))
{
continue;
}
var peak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
transitionIndex * originalHeader.NumPeaks + iPeak);
if (peak.StartTime < minimizedChromGroup.OptimizedStartTime.Value ||
peak.EndTime > minimizedChromGroup.OptimizedEndTime.Value)
{
outsideRange = true;
break;
}
}
if (!outsideRange)
{
retainedPeakIndexes.Add(iPeak);
}
}
}
else
{
retainedPeakIndexes.UnionWith(Enumerable.Range(0, originalHeader.NumPeaks));
}
int numPeaks = retainedPeakIndexes.Count;
int maxPeakIndex;
if (retainedPeakIndexes.Contains(originalHeader.MaxPeakIndex))
{
maxPeakIndex = retainedPeakIndexes.Count(index => index < originalHeader.MaxPeakIndex);
}
else
{
maxPeakIndex = -1;
}
long location = _outputStream.Position;
float[] times = originalChromGroup.Times.Skip(minimizedChromGroup.OptimizedFirstScan).Take(numPoints).ToArray();
List <float[]> intensities = new List <float[]>();
List <short[]> massError10Xs = originalChromGroup.MassError10XArray != null
? new List <short[]>()
: null;
int[][] scanIndexes = null;
if (originalChromGroup.ScanIndexes != null)
{
scanIndexes = new int[originalChromGroup.ScanIndexes.Length][];
for (int i = 0; i < scanIndexes.Length; i++)
{
if (originalChromGroup.ScanIndexes[i] != null)
{
scanIndexes[i] =
originalChromGroup.ScanIndexes[i].Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints)
.ToArray();
}
}
}
foreach (var originalIndex in minimizedChromGroup.RetainedTransitionIndexes)
{
_transitions.Add(_originalCache.GetTransition(originalIndex + originalHeader.StartTransitionIndex));
for (int originalPeakIndex = 0; originalPeakIndex < originalHeader.NumPeaks; originalPeakIndex++)
{
if (!retainedPeakIndexes.Contains(originalPeakIndex))
{
continue;
}
var originalPeak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
originalIndex * originalHeader.NumPeaks +
originalPeakIndex);
_peakCount++;
ChromPeak.WriteArray(_outputStreamPeaks.SafeFileHandle, new[] { originalPeak });
}
intensities.Add(originalChromGroup.IntensityArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
if (massError10Xs != null)
{
massError10Xs.Add(originalChromGroup.MassError10XArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
}
}
var massError10XArray = massError10Xs != null?massError10Xs.ToArray() : null;
byte[] points = ChromatogramCache.TimeIntensitiesToBytes(times, intensities.ToArray(), massError10XArray, scanIndexes);
// Compress the data (can be huge for AB data with lots of zeros)
byte[] pointsCompressed = points.Compress(3);
int lenCompressed = pointsCompressed.Length;
_outputStream.Write(pointsCompressed, 0, lenCompressed);
var header = new ChromGroupHeaderInfo5(originalHeader.Precursor,
originalHeader.TextIdIndex,
originalHeader.TextIdLen,
fileIndex,
_transitions.Count - startTransitionIndex,
startTransitionIndex,
numPeaks,
startPeakIndex,
startScoreIndex,
maxPeakIndex,
numPoints,
pointsCompressed.Length,
location,
originalHeader.Flags,
originalHeader.StatusId,
originalHeader.StatusRank);
_chromGroupHeaderInfos.Add(header);
}
private static long GetFileSize(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
return(CHROM_GROUP_HEADER_INFO_SIZE + chromGroupHeaderInfo.CompressedSize
+ chromGroupHeaderInfo.NumPeaks * chromGroupHeaderInfo.NumTransitions * PEAK_SIZE
+ chromGroupHeaderInfo.NumTransitions * TRANSITION_SIZE);
}
public MinimizedChromGroup(ChromGroupHeaderInfo5 chromGroupHeaderInfo)
{
ChromGroupHeaderInfo = chromGroupHeaderInfo;
OptimizedFirstScan = 0;
OptimizedLastScan = chromGroupHeaderInfo.NumPoints - 1;
}
