public bool GetChromatogram(ChromKey chromKey, out TimeIntensities timeIntensities)
{
int keyIndex = -1;
if (_chromKeyIndiceses != null)
{
var tolerance = (float)ChromTaskList.SrmDocument.Settings.TransitionSettings.Instrument.MzMatchTolerance;
keyIndex = _chromKeyIndiceses.IndexOf(entry => EqualsTolerant(chromKey, entry.Key, tolerance));
}
if (keyIndex == -1 || _chromKeyIndiceses == null) // Keep ReSharper from complaining
{
timeIntensities = null;
return(false);
}
ChromKeyIndices chromKeyIndices = _chromKeyIndiceses[keyIndex];
var chromGroupInfo = _chromatogramCache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
chromGroupInfo.ReadChromatogram(_chromatogramCache);
var tranInfo = chromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
if (tranInfo.TimeIntensities == null || tranInfo.TimeIntensities.NumPoints == 0)
{
// Chorus returns zero length chromatogram to indicate that no spectra matched
// the precursor filter.
timeIntensities = null;
return(false);
}
timeIntensities = CoalesceIntensities(tranInfo.TimeIntensities);
return(true);
}
public bool GetChromatogram(ChromKey chromKey, out float[] times, out int[] scanIds, out float[] intensities, out float[] massErrors)
{
int keyIndex = -1;
if (_chromKeyIndiceses != null)
{
var tolerance = (float)ChromTaskList.SrmDocument.Settings.TransitionSettings.Instrument.MzMatchTolerance;
Assume.IsNull(chromKey.OptionalMinTime);
Assume.IsNull(chromKey.OptionalMaxTime);
Assume.IsTrue(0 == chromKey.IonMobilityValue);
Assume.IsTrue(0 == chromKey.IonMobilityExtractionWidth);
keyIndex = _chromKeyIndiceses.IndexOf(entry => entry.Key.CompareTolerant(chromKey, tolerance) == 0);
}
if (keyIndex == -1 || _chromKeyIndiceses == null) // Keep ReSharper from complaining
{
times = null;
scanIds = null;
intensities = null;
massErrors = null;
return(false);
}
ChromKeyIndices chromKeyIndices = _chromKeyIndiceses[keyIndex];
var chromGroupInfo = _chromatogramCache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
chromGroupInfo.ReadChromatogram(_chromatogramCache);
var tranInfo = chromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
if (times.Length == 0)
{
// Chorus returns zero length chromatogram to indicate that no spectra matched
// the precursor filter.
times = null;
scanIds = null;
intensities = null;
massErrors = null;
return(false);
}
if (null != tranInfo.ScanIndexes)
{
scanIds = tranInfo.ScanIndexes[(short)chromKeyIndices.Key.Source];
}
else
{
scanIds = null;
}
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
CoalesceIntensities(ref times, ref scanIds, ref intensities, ref massErrors);
return(true);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color peptideColor, out ChromExtra extra, out TimeIntensities timeIntensities)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
timeIntensities = tranInfo.TimeIntensities;
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
return(true);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
massErrors = tranInfo.MassError10Xs.Select(m => m/10.0f).ToArray();
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
scanIndexes = tranInfo.ScanIndexes[(int) chromKeyIndices.Key.Source];
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return true;
}
