public Chromatogram(MzKey mzKey, double mz)
{
MzKey = mzKey;
Mz = mz;
Intensities = new List <float>();
PeakMzs = new List <float>();
}
protected void ShowChromatograms()
{
if (MsGraphControl.GraphPane == null)
{
// TODO: How can this happen?
return;
}
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
var selectedCharges = gridIntensities.GetSelectedCharges();
var selectedMasses = gridIntensities.GetSelectedMasses();
var chromatograms = PeptideFileAnalysis.ChromatogramSet;
var mzRanges = PeptideFileAnalysis.TurnoverCalculator.GetMzs(0);
var monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
if (selectedCharges.Count > 0 && !selectedCharges.Contains(charge))
{
continue;
}
for (int iMass = 0; iMass < PeptideAnalysis.GetMassCount(); iMass++)
{
var mzKey = new MzKey(charge, iMass);
double massDifference = mzRanges[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
if (selectedMasses.Count > 0)
{
if (!selectedMasses.Contains(iMass))
{
continue;
}
}
else
{
if (ExcludedMasses.IsExcluded(mzKey.MassIndex))
{
continue;
}
}
ChromatogramSetData.Chromatogram chromatogram;
if (!chromatograms.Chromatograms.TryGetValue(mzKey, out chromatogram))
{
continue;
}
var graphItem = new ChromatogramGraphItem
{
Title = label,
};
graphItem.Color = TracerChromatogramForm.GetColor(iMass, PeptideAnalysis.GetMassCount());
var mzRange = PeptideFileAnalysis.TurnoverCalculator.GetMzs(mzKey.Charge)[mzKey.MassIndex];
var massAccuracy = PeptideAnalysis.GetMassAccuracy();
var intensities = chromatogram.ChromatogramPoints.Select(point => point.GetIntensity(mzRange, massAccuracy)).ToArray();
if (Smooth)
{
intensities = TracerChromatograms.SavitzkyGolaySmooth(intensities);
}
PointPairList points = new PointPairList(chromatograms.Times, intensities);
graphItem.Points = points;
var lineItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, graphItem);
lineItem.Line.Style = TracerChromatogramForm.GetDashStyle(charge - PeptideAnalysis.MinCharge);
lineItem.Line.Width = Settings.Default.ChromatogramLineWidth;
lineItem.Label.IsVisible = false;
}
}
}
protected void ShowChromatograms()
{
if (MsGraphControl.GraphPane == null)
{
// TODO: How can this happen?
return;
}
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
var selectedCharges = gridIntensities.GetSelectedCharges();
var selectedMasses = gridIntensities.GetSelectedMasses();
var chromatograms = PeptideFileAnalysis.ChromatogramSet;
var mzRanges = PeptideFileAnalysis.TurnoverCalculator.GetMzs(0);
var monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
if (selectedCharges.Count > 0 && !selectedCharges.Contains(charge))
{
continue;
}
for (int iMass = 0; iMass < PeptideAnalysis.GetMassCount(); iMass++)
{
var mzKey = new MzKey(charge, iMass);
double massDifference = mzRanges[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
if (selectedMasses.Count > 0)
{
if (!selectedMasses.Contains(iMass))
{
continue;
}
}
else
{
if (ExcludedMasses.IsExcluded(mzKey.MassIndex))
{
continue;
}
}
ChromatogramSetData.Chromatogram chromatogram;
if (!chromatograms.Chromatograms.TryGetValue(mzKey, out chromatogram))
{
continue;
}
var graphItem = new ChromatogramGraphItem
{
Title = label,
};
graphItem.Color = TracerChromatogramForm.GetColor(iMass, PeptideAnalysis.GetMassCount());
var mzRange = PeptideFileAnalysis.TurnoverCalculator.GetMzs(mzKey.Charge)[mzKey.MassIndex];
var massAccuracy = PeptideAnalysis.GetMassAccuracy();
var intensities = chromatogram.ChromatogramPoints.Select(point => point.GetIntensity(mzRange, massAccuracy)).ToArray();
if (Smooth)
{
intensities = TracerChromatograms.SavitzkyGolaySmooth(intensities);
}
PointPairList points = new PointPairList(chromatograms.Times, intensities);
graphItem.Points = points;
var lineItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, graphItem);
lineItem.Line.Style = TracerChromatogramForm.GetDashStyle(charge - PeptideAnalysis.MinCharge);
lineItem.Line.Width = Settings.Default.ChromatogramLineWidth;
lineItem.Label.IsVisible = false;
}
}
}
public Chromatogram(MzKey mzKey, MzRange mzRange)
{
MzKey = mzKey;
MzRange = mzRange;
Points = new List<ChromatogramPoint>();
}
public Chromatogram(MzKey mzKey, MzRange mzRange)
{
MzKey = mzKey;
MzRange = mzRange;
Points = new List <ChromatogramPoint>();
}
public Chromatogram(MzKey mzKey, double mz)
{
MzKey = mzKey;
Mz = mz;
Intensities = new List<float>();
PeakMzs = new List<float>();
}
