public SpectrumViewer(string filename, object index, string interpretation)
{
// Prepare the annotation
annotation = new PeptideFragmentationAnnotation(interpretation, 1, 2, false, true, false, false, true, false, false, true, false, true);
annotation.OptionsPanel.Dock = DockStyle.None;
annotation.OptionsPanel.Dock = DockStyle.Fill;
// Get the mass spectrum
spectrum = SpectrumCache.GetMassSpectrum(filename, index);
if (spectrum == null)
{
return;
}
// Add annotation to the mass spectrum and get a new graph control
spectrum.AnnotationList.Clear();
spectrum.AnnotationList.Add((IAnnotation)annotation);
graph = new MSGraphControl();
graph.AddGraphItem(graph.GraphPane, spectrum);
graph.Dock = DockStyle.Fill;
// Create new panels and add the graph and annotations
spectrumPanel = new Panel();
spectrumPanel.Controls.Add(graph);
spectrumPanel.Dock = DockStyle.None;
spectrumPanel.Dock = DockStyle.Fill;
annotationPanel = new Panel();
annotationPanel.Controls.Add(annotation.OptionsPanel);
annotationPanel.Dock = DockStyle.None;
annotationPanel.Dock = DockStyle.Fill;
fragmentationPanel = new Panel();
annotation.FragmentInfoGridView.Location = new Point(0, 0);
annotation.FragmentInfoGridView.ScrollBars = ScrollBars.Both;
annotation.FragmentInfoGridView.Dock = DockStyle.None;
annotation.FragmentInfoGridView.Dock = DockStyle.Fill;
annotation.FragmentInfoGridView.BorderStyle = BorderStyle.FixedSingle;
fragmentationPanel.Controls.Add(annotation.FragmentInfoGridView);
fragmentationPanel.Dock = DockStyle.None;
fragmentationPanel.Dock = DockStyle.Fill;
// Add the call back for refreshing
annotation.OptionsChanged += new EventHandler(OnOptionsChanged);
}
private void UpdateGraph()
{
if (_inUpdateGraph)
{
return;
}
try
{
_inUpdateGraph = true;
_msGraphControl.GraphPane.GraphObjList.Clear();
_msGraphControl.GraphPane.CurveList.Clear();
dataGridView1.Rows.Clear();
int charge;
try
{
charge = Convert.ToInt32(tbxCharge.Text);
tbxCharge.BackColor = Color.White;
}
catch
{
charge = 0;
tbxCharge.BackColor = Color.Red;
}
double massResolution;
try
{
massResolution = double.Parse(tbxMassResolution.Text);
tbxMassResolution.BackColor = Color.White;
}
catch
{
tbxMassResolution.BackColor = Color.Red;
massResolution = .01;
}
var sequence = tbxSequence.Text;
MassDistribution spectrum;
if (string.IsNullOrEmpty(sequence))
{
var formula = tbxFormula.Text;
var molecule = Molecule.Parse(formula);
if (molecule.Values.Sum() > 10000000)
{
tbxFormula.BackColor = Color.Red;
return;
}
try
{
spectrum = Workspace.GetAminoAcidFormulas().GetMassDistribution(molecule, charge);
tbxFormula.BackColor = Color.White;
}
catch
{
tbxFormula.BackColor = Color.Red;
return;
}
}
else
{
tbxFormula.Text = Workspace.GetAminoAcidFormulas().GetFormula(sequence).ToString();
var turnoverCalculator = new TurnoverCalculator(Workspace, sequence);
var aminoAcidFormulas = Workspace.GetAminoAcidFormulasWithTracers();
aminoAcidFormulas = aminoAcidFormulas.SetMassResolution(massResolution);
try
{
if (cbxTracerPercents.Checked)
{
var tracerPercentFormula = TracerPercentFormula.Parse(tbxTracerFormula.Text);
spectrum = turnoverCalculator.GetAminoAcidFormulas(tracerPercentFormula)
.GetMassDistribution(sequence, charge);
}
else
{
var tracerFormula = TracerFormula.Parse(tbxTracerFormula.Text);
spectrum = aminoAcidFormulas.GetMassDistribution(
turnoverCalculator.MoleculeFromTracerFormula(tracerFormula), charge);
double massShift = aminoAcidFormulas.GetMassShift(sequence);
if (charge > 0)
{
massShift /= charge;
}
spectrum = spectrum.OffsetAndDivide(massShift, 1);
}
tbxTracerFormula.BackColor = Color.White;
}
catch
{
tbxTracerFormula.BackColor = Color.Red;
spectrum = aminoAcidFormulas.GetMassDistribution(sequence, charge);
}
}
if (spectrum == null)
{
return;
}
var curveItem = _msGraphControl.AddGraphItem(_msGraphControl.GraphPane, new GraphItem
{
Title = "Intensity",
Color = Color.Black,
Points =
new PointPairList(
spectrum.Keys.
ToArray(),
spectrum.Values.
ToArray())
});
curveItem.Label.IsVisible = false;
_msGraphControl.AxisChange();
_msGraphControl.Invalidate();
var entries = spectrum.ToArray();
dataGridView1.Rows.Add(entries.Length);
for (int i = 0; i < entries.Count(); i++)
{
var row = dataGridView1.Rows[i];
row.Cells[colMass.Index].Value = entries[i].Key;
row.Cells[colIntensity.Index].Value = entries[i].Value;
}
}
finally
{
_inUpdateGraph = false;
}
}