private void DisplayScan()
{
if (this.reader == null)
{
return;
}
try
{
this.scan.ValidateComponent();
this.minPeakIntensity.ValidateComponent();
double rt = retentionTimes[this.scan.Value - 1];
PeakList <Peak> pkl = reader.GetPeakList(rt, this.minPeakIntensity.Value, topPeak.Value);
try
{
ZedGraphicExtension.ClearData(this.zgcScan, false);
var pplLight = new PointPairList();
pkl.ForEach(p => pplLight.Add(p.Mz, p.Intensity));
ZedGraphicExtension.AddIndividualLine(this.zgcScan, MyConvert.Format("Scan {0}", this.scan.Value), pplLight, Color.Blue, false);
if (reader.GetMsLevel(rt) == 2)
{
this.zgcScan.GraphPane.Title.Text = MyConvert.Format("Precursor MZ = {0:0.0000}", pkl.PrecursorMZ);
}
else
{
this.zgcScan.GraphPane.Title.Text = string.Empty;
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcScan);
}
StringBuilder sb = new StringBuilder();
pkl.ForEach(m => sb.AppendLine(MyConvert.Format("{0:0.0000}\t{1:0.00}", m.Mz, m.Intensity)));
txtPeaks.Text = sb.ToString();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
var pplRed = new PointPairList();
var pplGreen = new PointPairList();
var enabled = summary.ObservedEnvelopes.FindAll(m => m.Enabled);
enabled.ForEach(m =>
{
PointPairList ppl = m.IsSelected ? pplGreen : pplRed;
if (summary.SampleIsLight)
{
ppl.Add(new PointPair(m.HeavyIntensity, m.LightIntensity, 0.0, m));
}
else
{
ppl.Add(new PointPair(m.LightIntensity, m.HeavyIntensity, 0.0, m));
}
});
ZedGraphicExtension.ClearData(this.zgcGraph, false);
AddCurve(pplGreen, SilacQuantificationConstants.REFERENCE_COLOR);
AddCurve(pplRed, SilacQuantificationConstants.SAMPLE_COLOR);
var pplTotal = new PointPairList();
pplTotal.AddRange(pplRed);
pplTotal.AddRange(pplGreen);
if (pplTotal.Count > 0)
{
PointPairList line = ZedGraphicExtension.GetRegressionLine(pplTotal, summary.Ratio);
ZedGraphicExtension.AddDataToLine(this.zgcGraph, MyConvert.Format("Ratio = {0:0.0000}, Correlation = {1:0.0000}", summary.Ratio,
summary.RegressionCorrelation), line, SilacQuantificationConstants.IDENTIFIED_COLOR, false);
}
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
private void lvDirectories_SelectedIndexChanged(object sender, EventArgs e)
{
if (lvFiles.SelectedItems.Count > 0)
{
string log = lvFiles.SelectedItems[0].Text;
SequestLogFormat reader = new SequestLogFormat();
var counts = reader.ReadFromFile(log);
ZedGraphicExtension.ClearData(zgc, false);
GraphPane myPane = zgc.GraphPane;
// Set the titles and axis labels
myPane.Title.Text = "Sequest Node Distribution";
myPane.XAxis.Title.Text = "Node";
myPane.YAxis.Title.Text = "Count";
var str =
(from c in counts
orderby c.Key
select c.Key).ToArray();
var y =
(from c in counts
orderby c.Key
select(double) c.Value).ToArray();
BarItem myCurve = myPane.AddBar("NodeCount", null, y, Color.Blue);
// Draw the X tics between the labels instead of at the labels
myPane.XAxis.MajorTic.IsBetweenLabels = true;
// Set the XAxis labels
myPane.XAxis.Scale.TextLabels = str;
// Set the XAxis to Text type
myPane.XAxis.Type = AxisType.Text;
myPane.Legend.IsVisible = false;
ZedGraphicExtension.UpdateGraph(zgc);
}
}
public void Update(IIsotopicProfiles profiles)
{
ZedGraphicExtension.ClearData(this.zgcGraph, false);
try
{
foreach (var profile in profiles.GetIsotopicProfiles())
{
var ppl = new PointPairList();
for (int i = 0; i < profile.Profile.Count; i++)
{
ppl.Add((i + 1), profile.Profile[i].Intensity);
}
ZedGraphicExtension.AddDataToBar(this.zgcGraph, ppl, profile.DisplayName, profile.DisplayColor, true);
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.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");
}
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
double minMz = envelope.Light[0].Mz - 1.0;
double maxMz = envelope.Heavy[envelope.Heavy.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var pplLight = new PointPairList();
envelope.Light.ForEach(p => pplLight.Add(p.Mz, p.Intensity));
var pplHeavy = new PointPairList();
envelope.Heavy.ForEach(p => pplHeavy.Add(p.Mz, p.Intensity));
if (summary.SampleIsLight)
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplLight, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplHeavy, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
else
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplHeavy, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplLight, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
// Shift the text items up by 5 user scale units above the bars
const float shift = 5;
var ppl = new PointPairList();
ppl.AddRange(pplLight);
ppl.AddRange(pplHeavy);
for (int i = 0; i < ppl.Count; i++)
{
// format the label string to have 1 decimal place
string lab = ppl[i].X.ToString("0.00");
// create the text item (assumes the x axis is ordinal or text)
// for negative bars, the label appears just above the zero value
var text = new TextObj(lab, ppl[i].X, ppl[i].Y + shift);
// tell Zedgraph to use user scale units for locating the TextItem
text.Location.CoordinateFrame = CoordType.AxisXYScale;
// AlignH the left-center of the text to the specified point
text.Location.AlignH = AlignH.Left;
text.Location.AlignV = AlignV.Center;
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
// rotate the text 90 degrees
text.FontSpec.Angle = 90;
// add the TextItem to the list
zgcGraph.GraphPane.GraphObjList.Add(text);
}
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = new RawFileImpl(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Open(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.Light.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
pplRaw.Add(minMz, 0.0);
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
pplRaw.Add(maxMz, 0.0);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "PeakList From RawFile", pplRaw, SilacQuantificationConstants.IDENTIFIED_COLOR, true);
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.InitGraphPane(this.title, "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
panel.InitGraphPane(this.title + ", Scan=" + envelope.Scan.ToString(), "m/z", "Intensity", true, 0.0);
double minMz = envelope[0].Mz - 1.0;
double maxMz = envelope[envelope.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var ppl = new PointPairList();
envelope.ForEach(p => { if (p.Intensity > 0)
{
ppl.Add(p.Mz, p.Intensity);
}
});
panel.AddIndividualLine("Isotopic Envelope", ppl, Color.Red);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
var halfMax = (from env in envelope
select env.Intensity).Max() / 2;
ppl.Clear();
envelope.ForEach(p => { if (p.Intensity == 0)
{
ppl.Add(p.Mz, halfMax);
}
});
panel.AddIndividualLine("", ppl, defaultColor: Color.Red, dStyle: DashStyle.Dash);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Close();
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
panel.AddIndividualLine("PeakList From RawFile", pplRaw, Color.Blue);
panel.AddTextDown(pplRaw, 5, (m => m.X.ToString("0.0000")));
/*
* foreach (var p in ppl)
* {
* if (p.Y == 0)
* {
* double ppm = double.MaxValue;
* double ppmAbs = Math.Abs(ppm);
* foreach (var pp in pplRaw)
* {
* double ppmCur = PrecursorUtils.mz2ppm(pp.X, pp.X - p.X);
* double ppmCurAbs = Math.Abs(ppmCur);
* if (Math.Abs(ppmCur) < ppmAbs)
* {
* ppm = ppmCur;
* ppmAbs = ppmCurAbs;
* }
*
* if (pp.X > p.X)
* {
* break;
* }
* }
*
* p.Z = ppm;
* }
* }
*/
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}