private void OutputMassSpectrum(string outputFolder, XYData massSpectrumXYData, TargetBase target, SipperLcmsTargetedResult sipperLcmsTargetedResult)
{
var msGraphGenerator = new MSGraphControl();
msGraphGenerator.SymbolType = SymbolType.None;
if (massSpectrumXYData == null)
{
massSpectrumXYData = new XYData();
massSpectrumXYData.Xvalues = new double[] { 0, 1, 2, 3, 4, 5 };
massSpectrumXYData.Yvalues = new double[] { 0, 1, 2, 3, 4, 5 };
}
msGraphGenerator.GenerateGraph(massSpectrumXYData.Xvalues, massSpectrumXYData.Yvalues, target.MZ - 2,
target.MZ + 6);
var annotation = "fractionC13= " + sipperLcmsTargetedResult.PercentCarbonsLabelled.ToString("0.000") + "\n" +
"populationFraction= " + sipperLcmsTargetedResult.PercentPeptideLabelled.ToString("0.000");
msGraphGenerator.AddAnnotationRelativeAxis(annotation, 0.45, 0.05);
var outputFilename = Path.Combine(outputFolder, target.ID + "_MS.png");
msGraphGenerator.SaveGraph(outputFilename);
}
public MSGraphPane GetOrCreateGraphPane(MSGraphControl graphControl, PaneKey graphPaneKey)
{
var pane = GetGraphPane(graphControl, graphPaneKey);
if (null != pane)
{
return(pane);
}
if (GraphPaneKeys.Count == 0)
{
GraphPaneKeys.Add(graphPaneKey);
pane = graphControl.GraphPane;
ApplySettingsToGraphPane(pane);
return(pane);
}
int index = GraphPaneKeys.BinarySearch(graphPaneKey);
int iInsert = ~index;
var graphPane = InsertMsGraphPane(graphControl, iInsert);
GraphPaneKeys.Insert(iInsert, graphPaneKey);
using (var graphics = graphControl.CreateGraphics())
{
graphControl.MasterPane.SetLayout(graphics, PaneLayout.SingleColumn);
}
return(graphPane);
}
public static GraphHelper Attach(MSGraphControl msGraphControl)
{
GraphHelper graphHelper = new GraphHelper(msGraphControl);
msGraphControl.MasterPane.Border.IsVisible = false;
msGraphControl.GraphPane.Border.IsVisible = false;
msGraphControl.GraphPane.AllowCurveOverlap = true;
return(graphHelper);
}
public IsotopeDistributionForm(Workspace workspace) : base(workspace)
{
InitializeComponent();
_msGraphControl = new MSGraphControlEx {
Dock = DockStyle.Fill
};
_msGraphControl.GraphPane.XAxis.Title.Text = "M/Z";
_msGraphControl.GraphPane.YAxis.Title.Text = "Intensity";
colMass.DefaultCellStyle.Format = "0.######";
colIntensity.DefaultCellStyle.Format = "0.######";
splitContainer1.Panel2.Controls.Add(_msGraphControl);
}
public MSGraphPane GetGraphPane(MSGraphControl graphControl, PaneKey graphPaneKey)
{
if (!AllowSplitPanes)
{
return(graphControl.GraphPane);
}
int index = GraphPaneKeys.BinarySearch(graphPaneKey);
if (index >= 0)
{
return((MSGraphPane)graphControl.MasterPane.PaneList[index]);
}
return(null);
}
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 MSGraphPane InsertMsGraphPane(MSGraphControl graphControl, int iInsert)
{
var pane = new MSGraphPane
{
Border = { IsVisible = false },
AllowCurveOverlap = true,
};
ApplySettingsToGraphPane(pane);
var primaryPane = graphControl.GraphPane;
pane.CurrentItemType = primaryPane.CurrentItemType;
pane.ZoomStack.AddRange(primaryPane.ZoomStack);
var zoomState = new ZoomState(primaryPane, ZoomState.StateType.Zoom);
zoomState.ApplyState(pane);
pane.YAxis.Title.Text = primaryPane.YAxis.Title.Text;
pane.XAxis.Title.Text = primaryPane.XAxis.Title.Text;
graphControl.MasterPane.PaneList.Insert(iInsert, pane);
return(pane);
}
public OpenDataSourceDialog()
{
InitializeComponent();
listViewColumnSorter = new ListViewColumnSorter();
listView.ListViewItemSorter = listViewColumnSorter;
DialogResult = DialogResult.Cancel;
string[] sourceTypes = new string[]
{
"Any spectra format",
"mzML",
//"mzData",
"mzXML",
"mz5",
"Thermo RAW",
"Waters RAW",
"ABSciex WIFF",
//"Bruker/Agilent YEP",
//"Bruker BAF",
//"Bruker FID",
"Bruker Analysis",
"Agilent MassHunter",
"Mascot Generic",
"Bruker Data Exchange",
//"Sequest DTA"
};
sourceTypeComboBox.Items.AddRange(sourceTypes);
sourceTypeComboBox.SelectedIndex = 0;
ImageList smallImageList = new ImageList();
smallImageList.ColorDepth = ColorDepth.Depth32Bit;
smallImageList.Images.Add(Properties.Resources.folder);
smallImageList.Images.Add(Properties.Resources.file);
smallImageList.Images.Add(Properties.Resources.DataProcessing);
listView.SmallImageList = smallImageList;
TreeView tv = new TreeView();
tv.Indent = 8;
TreeNode lookInNode = tv.Nodes.Add("My Recent Documents", "My Recent Documents", 0, 0);
lookInNode.Tag = lookInNode.Text;
lookInComboBox.Items.Add(lookInNode);
TreeNode desktopNode = tv.Nodes.Add("Desktop", "Desktop", 1, 1);
desktopNode.Tag = desktopNode.Text;
lookInComboBox.Items.Add(desktopNode);
lookInNode = desktopNode.Nodes.Add("My Documents", "My Documents", 2, 2);
lookInNode.Tag = lookInNode.Text;
lookInComboBox.Items.Add(lookInNode);
TreeNode myComputerNode = desktopNode.Nodes.Add("My Computer", "My Computer", 3, 3);
myComputerNode.Tag = myComputerNode.Text;
lookInComboBox.Items.Add(myComputerNode);
lookInComboBox.SelectedIndex = 1;
lookInComboBox.IntegralHeight = false;
lookInComboBox.DropDownHeight = lookInComboBox.Items.Count * lookInComboBox.ItemHeight + 2;
ticGraphControl = new MSGraphControl()
{
Dock = DockStyle.Fill,
};
ticGraphControl.GraphPane.Legend.IsVisible = false;
ticGraphControl.Visible = false;
splitContainer1.Panel2.Controls.Add(ticGraphControl);
splitContainer1.Panel2Collapsed = false;
}
public OpenDataSourceDialog()
{
InitializeComponent();
listViewColumnSorter = new ListViewColumnSorter();
listView.ListViewItemSorter = listViewColumnSorter;
DialogResult = DialogResult.Cancel;
var sourceTypes = new List <string>();
foreach (var typeExtsPair in ReaderList.FullReaderList.getFileExtensionsByType())
{
if (typeExtsPair.Value.Count > 0) // e.g. exclude UNIFI
{
sourceTypes.Add(typeExtsPair.Key);
}
}
sourceTypes.Sort();
sourceTypes.Insert(0, "Any spectra format");
sourceTypeComboBox.Items.AddRange(sourceTypes.ToArray());
sourceTypeComboBox.SelectedIndex = 0;
ImageList smallImageList = new ImageList();
smallImageList.ColorDepth = ColorDepth.Depth32Bit;
smallImageList.Images.Add(Properties.Resources.folder);
smallImageList.Images.Add(Properties.Resources.file);
smallImageList.Images.Add(Properties.Resources.DataProcessing);
listView.SmallImageList = smallImageList;
TreeView tv = new TreeView();
tv.Indent = 8;
TreeNode lookInNode = tv.Nodes.Add("My Recent Documents", "My Recent Documents", 0, 0);
lookInNode.Tag = lookInNode.Text;
lookInComboBox.Items.Add(lookInNode);
TreeNode desktopNode = tv.Nodes.Add("Desktop", "Desktop", 1, 1);
desktopNode.Tag = desktopNode.Text;
lookInComboBox.Items.Add(desktopNode);
lookInNode = desktopNode.Nodes.Add("My Documents", "My Documents", 2, 2);
lookInNode.Tag = lookInNode.Text;
lookInComboBox.Items.Add(lookInNode);
TreeNode myComputerNode = desktopNode.Nodes.Add("My Computer", "My Computer", 3, 3);
myComputerNode.Tag = myComputerNode.Text;
lookInComboBox.Items.Add(myComputerNode);
lookInComboBox.SelectedIndex = 1;
lookInComboBox.IntegralHeight = false;
lookInComboBox.DropDownHeight = lookInComboBox.Items.Count * lookInComboBox.ItemHeight + 2;
ticGraphControl = new MSGraphControl()
{
Dock = DockStyle.Fill,
};
ticGraphControl.GraphPane.Legend.IsVisible = false;
ticGraphControl.Visible = false;
splitContainer1.Panel2.Controls.Add(ticGraphControl);
splitContainer1.Panel2Collapsed = false;
}
public const string scientificNotationFormatString = "0.0#####e0"; // Not L10N
public GraphHelper(MSGraphControl msGraphControl)
{
GraphControl = msGraphControl;
_displayState = new ErrorDisplayState();
}
/// <summary>
/// Selects a peptide and then changes chromatogram "Transform" and "Transition" settings.
/// </summary>
private void TestPeptide(PeptideGroupDocNode peptideGroup, PeptideDocNode peptide)
{
RunUI(() => SkylineWindow.SelectedPath = new IdentityPath(peptideGroup.Id, peptide.Id));
Settings.Default.SplitChromatogramGraph = false;
RunUI(() => SkylineWindow.SetDisplayTypeChrom(DisplayTypeChrom.all));
WaitForGraphs();
var graphChrom = FindOpenForm <GraphChromatogram>();
MSGraphControl graphControl = (MSGraphControl)graphChrom.Controls.Find("graphControl", true).First();
if (peptide.TransitionGroupCount <= 1)
{
// When a peptide with one transition group is seleted, then all transitions should be displayed
Assert.AreEqual(peptide.TransitionCount, GetChromatogramCount(graphControl.GraphPane));
}
else
{
// If the peptide has more than one transition group, then only transition groups are displayed
// when the peptide is selected.
Assert.AreEqual(peptide.TransitionGroupCount, GetChromatogramCount(graphControl.GraphPane));
}
// When Display Type is set to "total", there is one curve per transition group.
RunUI(() => SkylineWindow.SetDisplayTypeChrom(DisplayTypeChrom.total));
WaitForGraphs();
Assert.AreEqual(peptide.TransitionGroupCount, GetChromatogramCount(graphControl.GraphPane));
foreach (var transitionGroup in peptide.TransitionGroups)
{
string message = peptide.ModifiedTarget.ToString() + ' ' + transitionGroup.PrecursorMz + ' ' + Settings.Default.TransformTypeChromatogram;
var transitionGroupPath = new IdentityPath(peptideGroup.Id, peptide.Id, transitionGroup.Id);
RunUI(() => SkylineWindow.SelectedPath = transitionGroupPath);
// Verify that "Split Graph" produces the correct number of panes.
Settings.Default.SplitChromatogramGraph = true;
RunUI(() => SkylineWindow.SetDisplayTypeChrom(DisplayTypeChrom.all));
WaitForGraphs();
if (transitionGroup.GetMsTransitions(true).Any() && transitionGroup.GetMsMsTransitions(true).Any())
{
Assert.AreEqual(2, graphControl.MasterPane.PaneList.Count, message);
}
else
{
Assert.AreEqual(1, graphControl.MasterPane.PaneList.Count, message);
}
int countTrans = 0;
foreach (var transition in transitionGroup.Transitions)
{
if (++countTrans >= 5) // Selecting absolutely everything makes this a pretty long test (this cuts time in half)
{
break;
}
var transitionPath = new IdentityPath(transitionGroupPath, transition.Id);
RunUI(() => SkylineWindow.SelectedPath = transitionPath);
RunUI(() => SkylineWindow.SetDisplayTypeChrom(DisplayTypeChrom.single));
WaitForGraphs();
Assert.AreEqual(1, graphControl.MasterPane.PaneList.Count);
if (1 != GetChromatogramCount(graphControl.GraphPane))
{
Assert.AreEqual(1, GetChromatogramCount(graphControl.GraphPane));
}
RunUI(() => SkylineWindow.SetDisplayTypeChrom(DisplayTypeChrom.total));
}
}
}
