public void UpdateGrid()
{
double monoisotopicMass =
Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
var masses = PeptideAnalysis.GetTurnoverCalculator().GetMzs(0);
if (MassColumn == null)
{
MassColumn = new DataGridViewTextBoxColumn
{
HeaderText = "Mass",
Name = "colMass",
Width = 60,
ReadOnly = true,
};
Columns.Add(MassColumn);
}
if (ExcludedColumn == null)
{
ExcludedColumn = new DataGridViewCheckBoxColumn
{
HeaderText = "Excluded",
Name = "colExcluded",
Width = 50,
SortMode = DataGridViewColumnSortMode.NotSortable,
};
Columns.Add(ExcludedColumn);
}
if (Rows.Count != PeptideAnalysis.GetMassCount())
{
Rows.Clear();
Rows.Add(PeptideAnalysis.GetMassCount());
for (int iRow = 0; iRow < Rows.Count; iRow++)
{
Rows[iRow].Tag = iRow;
}
}
for (int iRow = 0; iRow < Rows.Count; iRow++)
{
var row = Rows[iRow];
var iMass = (int)row.Tag;
double massDifference = masses[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
row.Cells[MassColumn.Index].Value = label;
row.Cells[MassColumn.Index].ToolTipText = "Mass:" + masses[iMass];
row.Cells[MassColumn.Index].Style.BackColor = TracerChromatogramForm.GetColor(iRow, Rows.Count);
row.Cells[ExcludedColumn.Index].Value = ExcludedMasses.IsMassExcluded(iMass);
}
}
protected virtual ICollection <int> GetSelectedMasses()
{
var result = new List <int>();
int massCount = PeptideAnalysis.GetMassCount();
for (int i = 0; i < massCount; i++)
{
result.Add(i);
}
return(result);
}
void DisplaySpectrum(int scanIndex)
{
if (!TopographForm.Instance.EnsureMsDataFile(PeptideFileAnalysis.MsDataFile, true))
{
return;
}
SpectrumForm spectrumForm;
spectrumForm = new SpectrumForm(PeptideFileAnalysis.MsDataFile)
{
ScanIndex = scanIndex,
};
spectrumForm.SetPeptideAnalysis(PeptideAnalysis);
spectrumForm.Show(TopLevelControl);
double minMz = 2000;
double maxMz = 0;
var selectedCharges = GetSelectedCharges();
var selectedMasses = GetSelectedMasses();
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++)
{
if (selectedMasses.Count > 0 && !selectedMasses.Contains(iMass))
{
continue;
}
var mzRange = PeptideAnalysis.GetMzs()[charge][iMass];
minMz = Math.Min(minMz, mzRange.Min);
maxMz = Math.Max(maxMz, mzRange.Max);
}
}
if (minMz <= maxMz)
{
spectrumForm.Zoom(minMz - 1, maxMz + 1);
}
}
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;
}
}
}
