public override bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities)
{
// No mass errors in SRM
if (_readChromatograms == 0)
{
_readStartTime = DateTime.UtcNow; // Said to be 117x faster than Now and this is for a delta
}
float[] times, intensities;
if (!_globalChromatogramExtractor.GetChromatogram(id, out times, out intensities))
{
_dataFile.GetChromatogram(id, out string chromId, out times, out intensities);
}
timeIntensities = new TimeIntensities(times, intensities, null, null);
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
if (!System.Diagnostics.Debugger.IsAttached)
{
double predictedMinutes = ExpectedReadDurationMinutes;
if (_readMaxMinutes > 0 && predictedMinutes > _readMaxMinutes)
{
// TODO: This warning isn't checked in the command line version of Skyline. Maybe we should do that.
if (Status is ChromatogramLoadingStatus)
{
Status =
((ChromatogramLoadingStatus)Status).ChangeWarningMessage(Resources.ChromatogramDataProvider_GetChromatogram_This_import_appears_to_be_taking_longer_than_expected__If_importing_from_a_network_drive__consider_canceling_this_import__copying_to_local_disk_and_retrying_);
}
}
}
if (_readChromatograms < _chromIds.Count)
{
SetPercentComplete(50 + _readChromatograms * 50 / _chromIds.Count);
}
int index = _chromIndices[id];
extra = new ChromExtra(index, -1); // TODO: is zero the right value?
// Display in AllChromatogramsGraph
var loadingStatus = Status as ChromatogramLoadingStatus;
if (loadingStatus != null)
{
loadingStatus.Transitions.AddTransition(
modifiedSequence,
color,
index, -1,
times,
intensities);
}
return(true);
}
public void ShimadzuFileTypeTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string extRaw = ExtensionTestContext.ExtShimadzuRaw;
// Do file type check
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("BSA-digest__MRM_optimisation_SL_scheduled_001" + extRaw)))
{
Assert.IsTrue(msData.IsShimadzuFile);
// check time is minutes
msData.GetChromatogram(msData.ChromatogramCount - 1, out _, out float[] times, out _);
Assert.AreEqual(new KeyValuePair <float, float>(5.908167f, 8.905833f), new KeyValuePair <float, float>(times.First(), times.Last()));
}
}
public bool GetChromatogram(int index, out float[] times, out float[] intensities)
{
index -= IndexOffset;
if (QcTraceByIndex.TryGetValue(index, out MsDataFileImpl.QcTrace qcTrace))
{
times = MsDataFileImpl.ToFloatArray(qcTrace.Times);
intensities = MsDataFileImpl.ToFloatArray(qcTrace.Intensities);
}
else if (index == TicChromatogramIndex || index == BpcChromatogramIndex)
{
_dataFile.GetChromatogram(index, out _, out times, out intensities, true);
}
else
{
times = intensities = null;
}
return(times != null);
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities)
{
float[] times, intensities;
if (!_globalChromatogramExtractor.GetChromatogram(id, out times, out intensities))
{
_dataFile.GetChromatogram(id, out _, out times, out intensities);
}
timeIntensities = new TimeIntensities(times, intensities, null, null);
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
if (_readChromatograms < _chromIds.Count)
{
SetPercentComplete(50 + _readChromatograms * 50 / _chromIds.Count);
}
int index = _chromIndices[id];
extra = new ChromExtra(index, -1); // TODO: is zero the right value?
// Display in AllChromatogramsGraph
var loadingStatus = Status as ChromatogramLoadingStatus;
if (loadingStatus != null)
{
loadingStatus.Transitions.AddTransition(
modifiedSequence,
color,
index, -1,
times,
intensities);
}
return(true);
}
public void Redisplay()
{
if (!IsHandleCreated)
{
return;
}
if (_inRedisplay)
{
return;
}
try
{
_inRedisplay = true;
tbxMinCharge.Text = MinCharge.ToString();
tbxMaxCharge.Text = MaxCharge.ToString();
tbxPeptideSequence.Text = PeptideSequence;
cbxShowPeptideMzs.Enabled = !string.IsNullOrEmpty(PeptideSequence);
tbxMassAccuracy.Text = MassAccuracy.ToString();
TurnoverCalculator turnoverCalculator = null;
if (!string.IsNullOrEmpty(PeptideSequence))
{
turnoverCalculator = new TurnoverCalculator(Workspace, PeptideSequence);
}
msGraphControlEx1.GraphPane.GraphObjList.Clear();
msGraphControlEx1.GraphPane.CurveList.Clear();
if (_spectrumData == null || comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
if (comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
string chromatogramName;
float[] timeArray;
float[] intensityArray;
msDataFileImpl.GetChromatogram(comboChromatogram.SelectedIndex, out chromatogramName, out timeArray, out intensityArray);
_chromatogramDatas[comboChromatogram.SelectedIndex] = new ChromatogramData(chromatogramName, timeArray, intensityArray);
}
_spectrumData = _spectrumData ?? new SpectrumData(msDataFileImpl, ScanIndex);
}
}
ChromatogramData chromatogram = null;
if (comboChromatogram.SelectedIndex >= 0)
{
chromatogram = _chromatogramDatas[comboChromatogram.SelectedIndex];
}
tbxMsLevel.Text = _spectrumData.MsLevel.ToString();
tbxTime.Text = _spectrumData.Time.ToString();
if (chromatogram != null && ScanIndex < chromatogram.TimeArray.Length)
{
tbxChromatogramRetentionTime.Text = chromatogram.TimeArray[ScanIndex].ToString();
tbxChromatogramIonCurrent.Text = chromatogram.IntensityArray[ScanIndex].ToString(NumberFormat);
}
else
{
tbxChromatogramRetentionTime.Text = tbxChromatogramIonCurrent.Text = @"N/A";
}
if (cbxShowProfile.Checked && _spectrumData.ProfileMzs != null)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, new SpectrumGraphItem()
{
Points =
new PointPairList(_spectrumData.ProfileMzs,
_spectrumData.ProfileIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.line,
Color = Color.Blue,
});
}
if (_spectrumData.ProfileIntensities != null)
{
tbxSumOfProfileIntensities.Text = _spectrumData.ProfileIntensities.Sum().ToString(NumberFormat);
}
else
{
tbxSumOfProfileIntensities.Text = "";
}
tbxCentroidIntensitySum.Text = _spectrumData.CentroidIntensities.Sum().ToString(NumberFormat);
var spectrum = new SpectrumGraphItem
{
Points = new PointPairList(_spectrumData.CentroidMzs, _spectrumData.CentroidIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.stick,
Color = Color.Black
};
if (turnoverCalculator != null)
{
var mzRanges = new Dictionary <MzRange, String>();
double monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideSequence);
double peptideIntensity = 0.0;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
foreach (var mzRange in turnoverCalculator.GetMzs(charge))
{
double mass = (mzRange.Center - AminoAcidFormulas.ProtonMass) * charge;
double massDifference = mass - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
mzRanges.Add(mzRange, label);
var chromatogramPoint = MsDataFileUtil.GetPoint(mzRange, _spectrumData.CentroidMzs, _spectrumData.CentroidIntensities);
peptideIntensity += chromatogramPoint.GetIntensity(mzRange, MassAccuracy);
}
}
spectrum.MassAccuracy = MassAccuracy;
spectrum.MzRanges = mzRanges;
tbxPeptideIntensity.Text = peptideIntensity.ToString(NumberFormat);
}
if (cbxShowCentroids.Checked)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, spectrum);
}
if (turnoverCalculator != null && cbxShowPeptideMzs.Checked)
{
double massAccuracy = MassAccuracy;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
var height = int.MaxValue;
foreach (var mzRange in mzs)
{
double min = mzRange.MinWithMassAccuracy(massAccuracy);
double max = mzRange.MaxWithMassAccuracy(massAccuracy);
msGraphControlEx1.GraphPane.GraphObjList.Add(new BoxObj(min, height, max - min, height, Color.Goldenrod, Color.Goldenrod)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
});
}
}
}
msGraphControlEx1.Invalidate();
}
finally
{
_inRedisplay = false;
}
}
