protected override void OnHandleCreated(EventArgs e)
{
base.OnHandleCreated(e);
if (Workspace == null)
{
return;
}
if (_tracerChromatogramForm == null)
{
_tracerChromatogramForm = new TracerChromatogramForm(PeptideFileAnalysis)
{
CloseButton = false
};
_tracerChromatogramForm.Show(_dockPanel, DockState.Document);
}
if (_chromatogramForm == null)
{
_chromatogramForm = new ChromatogramForm(PeptideFileAnalysis)
{
CloseButton = false
};
_chromatogramForm.Show(_dockPanel, DockState.Document);
}
if (_precursorPoolForm == null)
{
_precursorPoolForm = new PrecursorPoolForm(PeptideFileAnalysis)
{
CloseButton = false,
};
_precursorPoolForm.Show(_dockPanel, DockState.Document);
}
UpdateForm();
}
private void RefreshUi()
{
if (_inRefreshUi)
{
return;
}
try
{
_inRefreshUi = true;
_zedGraphControl.GraphPane.CurveList.Clear();
_zedGraphControl.GraphPane.GraphObjList.Clear();
if (_queryRows == null)
{
return;
}
var values = new Dictionary <CohortKey, double[]>();
var xValues = new double[101];
for (int i = 0; i < xValues.Length; i++)
{
xValues[i] = i;
}
foreach (var row in _queryRows)
{
double[] vector;
if (!values.TryGetValue(row.Key, out vector))
{
vector = new double[xValues.Length];
values.Add(row.Key, vector);
}
foreach (var entry in row.Value)
{
if (entry.Key < 0 || entry.Key > 1)
{
continue;
}
vector[(int)Math.Round(entry.Key * 100)] += entry.Value;
}
}
var cohortKeys = new List <CohortKey>(values.Keys);
cohortKeys.Sort();
if (dataGridView1.Rows.Count != cohortKeys.Count)
{
dataGridView1.Rows.Clear();
dataGridView1.Rows.Add(cohortKeys.Count);
}
for (int i = 0; i < cohortKeys.Count; i++)
{
var cohortKey = cohortKeys[i];
var yValues = values[cohortKey];
var row = dataGridView1.Rows[i];
if (dataGridView1.SelectedRows.Count == 0 || dataGridView1.SelectedRows.Contains(row))
{
_zedGraphControl.GraphPane.AddBar(cohortKey.ToString(), xValues, yValues, TracerChromatogramForm.GetColor(i, cohortKeys.Count));
}
row.Cells[colCohort.Index].Value = cohortKey;
var statsX = new Statistics(xValues);
var statsY = new Statistics(yValues);
row.Cells[colMean.Index].Value = statsX.Mean(statsY);
row.Cells[colStdDev.Index].Value = statsX.StdDev(statsY);
row.Cells[colMedian.Index].Value = statsX.Median(statsY);
}
_zedGraphControl.GraphPane.AxisChange();
_zedGraphControl.Invalidate();
}
finally
{
_inRefreshUi = 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;
}
}
}
private void UpdateGraph()
{
zedGraphControl.GraphPane.CurveList.Clear();
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.Title.IsVisible = false;
MsDataFile normalizeTo = null;
var fileAnalyses = new List <PeptideFileAnalysis>();
for (int iRow = 0; iRow < dataGridView.Rows.Count; iRow++)
{
fileAnalyses.Add((PeptideFileAnalysis)dataGridView.Rows[iRow].Tag);
}
if (fileAnalyses.Count == 0)
{
return;
}
if (_normalizeRetentionTimes)
{
normalizeTo = fileAnalyses[0].MsDataFile;
}
var tracerFormulas = PeptideAnalysis.GetTurnoverCalculator().ListTracerFormulas();
var pointPairLists = tracerFormulas.Select(tf => new PointPairList()).ToArray();
for (int iFileAnalysis = 0; iFileAnalysis < fileAnalyses.Count; iFileAnalysis++)
{
var fileAnalysis = fileAnalyses[iFileAnalysis];
var peaks = fileAnalysis.CalculatedPeaks;
if (peaks == null)
{
continue;
}
for (int iTracerFormula = 0; iTracerFormula < tracerFormulas.Count; iTracerFormula++)
{
var pointPairList = pointPairLists[iTracerFormula];
var peak = peaks.GetPeak(tracerFormulas[iTracerFormula]);
if (peak == null)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, PointPairBase.Missing, PointPairBase.Missing));
}
else
{
if (normalizeTo == null)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, peak.Value.EndTime, peak.Value.StartTime));
}
else
{
var alignment = fileAnalysis.MsDataFile.GetRetentionTimeAlignment(normalizeTo);
if (alignment.IsInvalid)
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, PointPairBase.Missing, PointPairBase.Missing));
}
else
{
pointPairList.Add(new PointPair(iFileAnalysis + 1, alignment.GetTargetTime(peak.Value.EndTime), alignment.GetTargetTime(peak.Value.StartTime), fileAnalysis));
}
}
}
}
}
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels =
fileAnalyses.Select(fileAnalysis => fileAnalysis.MsDataFile.ToString()).ToArray();
zedGraphControl.GraphPane.XAxis.Title.Text = "Data File";
zedGraphControl.GraphPane.YAxis.Title.Text = normalizeTo == null ? "Retention Time" : "Normalized Retention Time";
for (int iTracerFormula = 0; iTracerFormula < tracerFormulas.Count; iTracerFormula++)
{
zedGraphControl.GraphPane.AddHiLowBar(tracerFormulas[iTracerFormula].ToDisplayString(),
pointPairLists[iTracerFormula],
TracerChromatogramForm.GetColor(iTracerFormula,
tracerFormulas.Count));
}
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
}
