public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
panel.ClearData();
var summary = e.Item as IsobaricItem;
if (null != summary)
{
if (summary.PeakInIsolationWindow.Count > 0)
{
var pplWinPrecursor = new PointPairList();
foreach (var peak in summary.PeakInIsolationWindow)
{
if (peak.Tag > 0)
{
pplWinPrecursor.Add(new PointPair(peak.Mz, peak.Intensity, string.Format("{0:0.00000}", peak.Mz)));
}
else
{
pplWinPrecursor.Add(new PointPair(peak.Mz, peak.Intensity));
}
}
panel.AddIndividualLine("", pplWinPrecursor, Color.Black, Color.Blue);
panel.Title.Text = string.Format("Isolation Window (Specifity = {0:0.00}%)", summary.PrecursorPercentage * 100);
}
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
private void AddIonSeries(GraphPane peakPane, GraphPane ppmPane, PeakList <MatchedPeak> mgf, double mzTolerance, double minIntensity, IPeptideFragmentationBuilder <MatchedPeak> builder, string sequence, Color tagColor)
{
MatchedPeakUtils.Match(mgf, builder.Build(sequence), mzTolerance, minIntensity);
var ionType = builder.SeriesType.ToString();
var matchedIons = (from m in mgf
where m.Matched && m.PeakType == builder.SeriesType
select m).ToList();
var ppl = new PointPairList();
foreach (var m in matchedIons)
{
ppl.Add(new PointPair(m.Mz, m.Intensity, m.Information));
}
peakPane.AddIndividualLine("", ppl, Color.Black, tagColor);
if (ppmPane != null)
{
var diff = new PointPairList();
foreach (var m in matchedIons)
{
if (isPPM)
{
diff.Add(new PointPair(m.Mz, PrecursorUtils.mz2ppm(m.Mz, m.Mz - m.MatchedMZ)));
}
else
{
diff.Add(new PointPair(m.Mz, m.Mz - m.MatchedMZ));
}
}
ppmPane.AddPoints(diff, tagColor);
}
}
private void AddUnmatchedIons(GraphPane peakPane, PeakList <MatchedPeak> mgf)
{
var matchedIons = (from m in mgf
where !m.Matched
select m).ToList();
var ppl = new PointPairList();
foreach (var m in matchedIons)
{
ppl.Add(new PointPair(m.Mz, m.Intensity));
}
peakPane.AddIndividualLine("", ppl, Color.Black);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
panel.ClearData();
var summary = e.Item as IsobaricItem;
if (null != summary)
{
var pplData = new PointPairList();
if (summary.RawPeaks.Count > 0)
{
foreach (var peak in summary.RawPeaks)
{
pplData.Add(new PointPair(peak.Mz, peak.Intensity));
}
}
else
{
var definitions = summary.Definition.Items;
foreach (var def in definitions)
{
pplData.Add(new PointPair(def.Index, summary[def.Index]));
}
}
panel.AddIndividualLine("", pplData, Color.Black);
panel.XAxis.Scale.Min = summary.Definition.MinIndex - 1;
panel.XAxis.Scale.Max = summary.Definition.MaxIndex + 1;
panel.Title.Text = string.Format("{0},{1}", summary.Experimental, summary.Scan);
}
if (updateGraph)
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
double sampleMz;
double referenceMz;
if (summary.SampleIsLight)
{
sampleMz = summary.ObservedEnvelopes[0].Light[0].Mz;
referenceMz = summary.ObservedEnvelopes[0].Heavy[0].Mz;
}
else
{
sampleMz = summary.ObservedEnvelopes[0].Heavy[0].Mz;
referenceMz = summary.ObservedEnvelopes[0].Light[0].Mz;
}
panel.ClearData();
var pplSample = new PointPairList();
var pplReference = new PointPairList();
var pplSampleCurve = new PointPairList();
var pplReferenceCurve = new PointPairList();
bool bChecked = false;
for (int i = 0; i < summary.ObservedEnvelopes.Count; i++)
{
var envelope = summary.ObservedEnvelopes[i];
if (envelope.Enabled != bChecked)
{
if (pplSampleCurve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplSampleCurve, SilacQuantificationConstants.SAMPLE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
panel.AddPoly("", pplReferenceCurve, SilacQuantificationConstants.REFERENCE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
}
}
pplSampleCurve = new PointPairList();
pplReferenceCurve = new PointPairList();
bChecked = envelope.Enabled;
}
if (summary.SampleIsLight)
{
pplSampleCurve.Add(envelope.Scan, envelope.LightIntensity);
pplReferenceCurve.Add(envelope.Scan, envelope.HeavyIntensity);
pplSample.Add(envelope.Scan, envelope.LightIntensity);
pplReference.Add(envelope.Scan, envelope.HeavyIntensity);
}
else
{
pplSampleCurve.Add(envelope.Scan, envelope.LightIntensity);
pplReferenceCurve.Add(envelope.Scan, envelope.HeavyIntensity);
pplSample.Add(envelope.Scan, envelope.HeavyIntensity);
pplReference.Add(envelope.Scan, envelope.LightIntensity);
}
}
if (pplSampleCurve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplSampleCurve, SilacQuantificationConstants.SAMPLE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
panel.AddPoly("", pplReferenceCurve, SilacQuantificationConstants.REFERENCE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
}
}
panel.AddCurve("Sample", pplSample, SilacQuantificationConstants.SAMPLE_COLOR, SymbolType.None);
panel.AddCurve("Reference", pplReference, SilacQuantificationConstants.REFERENCE_COLOR, SymbolType.None);
var identified = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsIdentified).ForEach(m =>
{
identified.Add(new PointPair(m.Scan, m.LightIntensity));
identified.Add(new PointPair(m.Scan, m.HeavyIntensity));
});
panel.AddIndividualLine("Identified", identified, SilacQuantificationConstants.IDENTIFIED_COLOR);
var currentScan = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsSelected).ForEach(m =>
{
currentScan.Add(new PointPair(m.Scan, Math.Max(m.LightIntensity, m.HeavyIntensity)));
});
if (currentScan.Count > 0)
{
panel.AddIndividualLine("CurrentScan", currentScan, Color.Black);
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
private void UpdateCurve()
{
foreach (GraphPane pane in zgcCurve.MasterPane.PaneList)
{
pane.ClearData();
}
try
{
if (lvPrecursor.SelectedItems.Count == 0)
{
return;
}
GraphPane graphScans = zgcCurve.MasterPane.PaneList[0];
GraphPane graphPPM = zgcCurve.MasterPane.PaneList[1];
var pplScan = new PointPairList();
var pplPPM = new PointPairList();
var pplScanCurve = new PointPairList();
bool bChecked = false;
double precursorMz = MyConvert.ToDouble(lvPrecursor.SelectedItems[0].Text);
var identified = new PointPairList();
foreach (ListViewItem item in this.lvScans.Items)
{
if (item == null)
{
return;
}
if (item.Checked != bChecked)
{
if (pplScanCurve.Count > 0 && bChecked)
{
graphScans.AddPoly("", pplScanCurve, Color.Blue, new[] { PLOY_COLOR });
}
pplScanCurve = new PointPairList();
bChecked = item.Checked;
}
LabelFreeItem c = (LabelFreeItem)item.Tag;
pplScan.Add(new PointPair(c.Scan, c.AdjustIntensity));
pplScanCurve.Add(new PointPair(c.Scan, c.AdjustIntensity));
pplPPM.Add(new PointPair(c.Scan, c.DeltaMzPPM));
if (c.Identified)
{
identified.Add(new PointPair(c.Scan, c.AdjustIntensity));
}
}
if (pplScanCurve.Count > 0 && bChecked)
{
graphScans.AddPoly("", pplScanCurve, Color.Blue, new[] { PLOY_COLOR });
}
graphScans.AddCurve(precursorMz.ToString(), pplScan, Color.Blue, SymbolType.None);
graphPPM.AddCurve(precursorMz.ToString(), pplPPM, Color.Blue, SymbolType.None);
graphScans.AddIndividualLine("Identified", identified, Color.Red);
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcCurve);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
try
{
int firstScan = summary.ObservedEnvelopes.First().Scan;
int lastScan = summary.ObservedEnvelopes.Last().Scan;
var samplePPMList = summary.GetSamplePPMList();
var refPPMList = summary.GetReferencePPMList();
var samplePPMs = GetPoints(firstScan, lastScan, samplePPMList);
var referencePPMs = GetPoints(firstScan, lastScan, refPPMList);
panel.AddCurve("Sample", samplePPMs, SilacQuantificationConstants.SAMPLE_COLOR, SymbolType.None);
panel.AddCurve("Reference", referencePPMs, SilacQuantificationConstants.REFERENCE_COLOR, SymbolType.None);
var identified = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsIdentified).ForEach(m =>
{
if (samplePPMList.ContainsKey(m))
{
identified.Add(new PointPair(m.Scan, samplePPMList[m]));
}
if (refPPMList.ContainsKey(m))
{
identified.Add(new PointPair(m.Scan, refPPMList[m]));
}
});
panel.AddIndividualLine("Identified", identified, SilacQuantificationConstants.IDENTIFIED_COLOR);
var selected = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsSelected).ForEach(m =>
{
if (samplePPMList.ContainsKey(m))
{
selected.Add(new PointPair(m.Scan, samplePPMList[m]));
}
if (refPPMList.ContainsKey(m))
{
selected.Add(new PointPair(m.Scan, refPPMList[m]));
}
});
if (selected.Count > 0)
{
panel.AddIndividualLine("CurrentScan", selected, Color.Black);
}
panel.YAxis.Scale.Min = -10;
panel.YAxis.Scale.Max = 10;
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
var pplO16 = new PointPairList();
var pplO18_1 = new PointPairList();
var pplO18_2 = new PointPairList();
var pplO16Curve = new PointPairList();
var pplO18_1Curve = new PointPairList();
var pplO18_2Curve = new PointPairList();
var identified = new PointPairList();
var currentScan = new PointPairList();
bool bChecked = false;
for (int i = 0; i < summary.ObservedEnvelopes.Count; i++)
{
var envelope = summary.ObservedEnvelopes[i];
if (envelope.Enabled != bChecked)
{
if (pplO16Curve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplO16Curve, O18QuantificationConstants.COLOR_O16, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_1Curve, O18QuantificationConstants.COLOR_O18_1, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_2Curve, O18QuantificationConstants.COLOR_O18_2, new[] { O18QuantificationConstants.COLOR_PLOY });
}
}
pplO16Curve = new PointPairList();
pplO18_1Curve = new PointPairList();
pplO18_2Curve = new PointPairList();
bChecked = envelope.Enabled;
}
pplO16.Add(envelope.Scan, envelope[0].Intensity);
pplO18_1.Add(envelope.Scan, envelope[2].Intensity);
pplO18_2.Add(envelope.Scan, envelope[4].Intensity);
pplO16Curve.Add(envelope.Scan, envelope[0].Intensity);
pplO18_1Curve.Add(envelope.Scan, envelope[2].Intensity);
pplO18_2Curve.Add(envelope.Scan, envelope[4].Intensity);
if (envelope.IsIdentified)
{
identified.Add(envelope.Scan, new double[] { envelope[0].Intensity, envelope[2].Intensity, envelope[4].Intensity }.Max());
}
if (envelope.IsSelected)
{
currentScan.Add(envelope.Scan, new double[] { envelope[0].Intensity, envelope[2].Intensity, envelope[4].Intensity }.Max());
}
}
if (pplO16Curve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplO16Curve, O18QuantificationConstants.COLOR_O16, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_1Curve, O18QuantificationConstants.COLOR_O18_1, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_2Curve, O18QuantificationConstants.COLOR_O18_2, new[] { O18QuantificationConstants.COLOR_PLOY });
}
}
panel.AddCurve("O16", pplO16, O18QuantificationConstants.COLOR_O16, SymbolType.None);
panel.AddCurve("O18(1)", pplO18_1, O18QuantificationConstants.COLOR_O18_1, SymbolType.None);
panel.AddCurve("O18(2)", pplO18_2, O18QuantificationConstants.COLOR_O18_2, SymbolType.None);
panel.AddIndividualLine("Identified", identified, O18QuantificationConstants.COLOR_IDENTIFIED);
panel.AddIndividualLine("CurrentScan", currentScan, Color.Black);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
