public void ShowSpectrum(IScanProvider scanProvider, int transitionIndex, int scanIndex)
{
_msDataFileScanHelper.UpdateScanProvider(scanProvider, transitionIndex, scanIndex);
if (scanProvider != null)
{
comboBoxScanType.Items.Clear();
foreach (var source in new[] { ChromSource.ms1, ChromSource.fragment, ChromSource.sim })
{
foreach (var transition in _msDataFileScanHelper.ScanProvider.Transitions)
{
if (transition.Source == source)
{
comboBoxScanType.Items.Add(_msDataFileScanHelper.NameFromSource(source));
break;
}
}
}
comboBoxScanType.SelectedIndexChanged -= comboBoxScanType_SelectedIndexChanged;
comboBoxScanType.SelectedItem = _msDataFileScanHelper.NameFromSource(_msDataFileScanHelper.Source);
comboBoxScanType.SelectedIndexChanged += comboBoxScanType_SelectedIndexChanged;
comboBoxScanType.Enabled = true;
LoadScan(true, true);
}
else
{
ClearGraph();
// No full scans can be displayed.
_graphHelper.SetErrorGraphItem(new UnavailableMSGraphItem());
}
UpdateUI(false);
}
public void UpdateUI(bool selectionChanged = true)
{
// Only worry about updates, if the graph is visible
// And make sure it is not disposed, since rendering happens on a timer
if (!Visible || IsDisposed)
{
return;
}
// Clear existing data from the graph pane
var graphPane = (MSGraphPane)graphControl.MasterPane[0];
graphPane.CurveList.Clear();
graphPane.GraphObjList.Clear();
GraphItem = null;
GraphHelper.FormatGraphPane(graphControl.GraphPane);
GraphHelper.FormatFontSize(graphControl.GraphPane, Settings.Default.SpectrumFontSize);
// Try to find a tree node with spectral library info associated
// with the current selection.
var nodeTree = _stateProvider.SelectedNode as SrmTreeNode;
var nodeGroupTree = nodeTree as TransitionGroupTreeNode;
var nodeTranTree = nodeTree as TransitionTreeNode;
if (nodeTranTree != null)
{
nodeGroupTree = nodeTranTree.Parent as TransitionGroupTreeNode;
}
var nodeGroup = (nodeGroupTree != null ? nodeGroupTree.DocNode : null);
PeptideTreeNode nodePepTree;
if (nodeGroup == null)
{
nodePepTree = nodeTree as PeptideTreeNode;
if (nodePepTree != null)
{
var listInfoGroups = GetLibraryInfoChargeGroups(nodePepTree);
if (listInfoGroups.Length == 1)
{
nodeGroup = listInfoGroups[0];
}
else if (listInfoGroups.Length > 1)
{
_nodeGroup = null;
toolBar.Visible = false;
_graphHelper.SetErrorGraphItem(new NoDataMSGraphItem(
Resources.GraphSpectrum_UpdateUI_Multiple_charge_states_with_library_spectra));
return;
}
}
}
else
{
nodePepTree = nodeGroupTree.Parent as PeptideTreeNode;
}
// Check for appropriate spectrum to load
SrmSettings settings = DocumentUI.Settings;
PeptideLibraries libraries = settings.PeptideSettings.Libraries;
bool available = false;
if (nodeGroup == null || (!nodeGroup.HasLibInfo && !libraries.HasMidasLibrary))
{
_spectra = null;
}
else
{
TransitionGroup group = nodeGroup.TransitionGroup;
TransitionDocNode transition = (nodeTranTree == null ? null : nodeTranTree.DocNode);
var lookupSequence = group.Peptide.Target;// Sequence or custom ion id
ExplicitMods lookupMods = null;
if (nodePepTree != null)
{
lookupSequence = nodePepTree.DocNode.SourceUnmodifiedTarget;
lookupMods = nodePepTree.DocNode.SourceExplicitMods;
}
try
{
// Try to load a list of spectra matching the criteria for
// the current node group.
if (libraries.HasLibraries && libraries.IsLoaded)
{
if (NodeGroupChanged(nodeGroup))
{
try
{
UpdateSpectra(nodeGroup, lookupSequence, lookupMods);
UpdateToolbar();
}
catch (Exception)
{
_spectra = null;
UpdateToolbar();
throw;
}
_nodeGroup = nodeGroup;
if (settings.TransitionSettings.Instrument.IsDynamicMin)
{
ZoomSpectrumToSettings();
}
}
var spectrum = SelectedSpectrum;
if (spectrum != null)
{
IsotopeLabelType typeInfo = spectrum.LabelType;
var types = _stateProvider.ShowIonTypes(group.IsProteomic);
var adducts = (group.IsProteomic ?
Transition.DEFAULT_PEPTIDE_LIBRARY_CHARGES :
nodeGroup.InUseAdducts).ToArray();
var charges = _stateProvider.ShowIonCharges(adducts);
var rankTypes = group.IsProteomic ? settings.TransitionSettings.Filter.PeptideIonTypes : settings.TransitionSettings.Filter.SmallMoleculeIonTypes;
var rankAdducts = group.IsProteomic ? settings.TransitionSettings.Filter.PeptideProductCharges : settings.TransitionSettings.Filter.SmallMoleculeFragmentAdducts;
var rankCharges = Adduct.OrderedAbsoluteChargeValues(rankAdducts);
// Make sure the types and charges in the settings are at the head
// of these lists to give them top priority, and get rankings correct.
int i = 0;
foreach (IonType type in rankTypes)
{
if (types.Remove(type))
{
types.Insert(i++, type);
}
}
i = 0;
var showAdducts = new List <Adduct>();
foreach (var charge in rankCharges)
{
if (charges.Remove(charge))
{
charges.Insert(i++, charge);
}
// NB for all adducts we just look at abs value of charge
// CONSIDER(bspratt): we may want finer per-adduct control for small molecule use
showAdducts.AddRange(adducts.Where(a => charge == Math.Abs(a.AdductCharge)));
}
showAdducts.AddRange(adducts.Where(a => charges.Contains(Math.Abs(a.AdductCharge)) && !showAdducts.Contains(a)));
SpectrumPeaksInfo spectrumInfo = spectrum.SpectrumPeaksInfo;
var spectrumInfoR = new LibraryRankedSpectrumInfo(spectrumInfo,
typeInfo,
nodeGroup,
settings,
lookupSequence,
lookupMods,
showAdducts,
types,
rankAdducts,
rankTypes);
GraphItem = new SpectrumGraphItem(nodeGroup, transition, spectrumInfoR, spectrum.LibName)
{
ShowTypes = types,
ShowCharges = charges,
ShowRanks = Settings.Default.ShowRanks,
ShowMz = Settings.Default.ShowIonMz,
ShowObservedMz = Settings.Default.ShowObservedMz,
ShowDuplicates = Settings.Default.ShowDuplicateIons,
FontSize = Settings.Default.SpectrumFontSize,
LineWidth = Settings.Default.SpectrumLineWidth
};
LibraryChromGroup chromatogramData = null;
if (Settings.Default.ShowLibraryChromatograms)
{
chromatogramData = spectrum.LoadChromatogramData();
}
if (null == chromatogramData)
{
_graphHelper.ResetForSpectrum(new[] { nodeGroup.TransitionGroup });
_graphHelper.AddSpectrum(GraphItem);
_graphHelper.ZoomSpectrumToSettings(DocumentUI, nodeGroup);
}
else
{
_graphHelper.ResetForChromatograms(new[] { nodeGroup.TransitionGroup });
var displayType = GraphChromatogram.GetDisplayType(DocumentUI, nodeGroup);
IList <TransitionDocNode> displayTransitions =
GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
int numTrans = displayTransitions.Count;
var allChromDatas =
chromatogramData.ChromDatas.Where(
chromData => DisplayTypeMatches(chromData, displayType)).ToList();
var chromDatas = new List <LibraryChromGroup.ChromData>();
for (int iTran = 0; iTran < numTrans; iTran++)
{
var displayTransition = displayTransitions[iTran];
var indexMatch =
allChromDatas.IndexOf(chromData => IonMatches(displayTransition.Transition, chromData));
if (indexMatch >= 0)
{
chromDatas.Add(allChromDatas[indexMatch]);
allChromDatas.RemoveAt(indexMatch);
}
else
{
chromDatas.Add(null);
}
}
allChromDatas.Sort((chromData1, chromData2) => chromData1.Mz.CompareTo(chromData2.Mz));
chromDatas.AddRange(allChromDatas);
double maxHeight = chromDatas.Max(chromData => null == chromData ? double.MinValue : chromData.Height);
int iChromDataPrimary = chromDatas.IndexOf(chromData => null != chromData && maxHeight == chromData.Height);
int colorOffset = displayType == DisplayTypeChrom.products
? GraphChromatogram.GetDisplayTransitions(nodeGroup,
DisplayTypeChrom.
precursors).Count()
: 0;
for (int iChromData = 0; iChromData < chromDatas.Count; iChromData++)
{
var chromData = chromDatas[iChromData];
if (chromData == null)
{
continue;
}
string label;
var pointAnnotation = GraphItem.AnnotatePoint(new PointPair(chromData.Mz, 1.0));
if (null != pointAnnotation)
{
label = pointAnnotation.Label;
}
else
{
label = chromData.Mz.ToString(@"0.####");
}
TransitionDocNode matchingTransition;
Color color;
if (iChromData < numTrans)
{
matchingTransition = displayTransitions[iChromData];
color =
GraphChromatogram.COLORS_LIBRARY[
(iChromData + colorOffset) % GraphChromatogram.COLORS_LIBRARY.Count];
}
else
{
matchingTransition = null;
color =
GraphChromatogram.COLORS_GROUPS[
iChromData % GraphChromatogram.COLORS_GROUPS.Count];
}
TransitionChromInfo tranPeakInfo;
ChromatogramInfo chromatogramInfo;
MakeChromatogramInfo(nodeGroup.PrecursorMz, chromatogramData, chromData, out chromatogramInfo, out tranPeakInfo);
var graphItem = new ChromGraphItem(nodeGroup, matchingTransition, chromatogramInfo, iChromData == iChromDataPrimary ? tranPeakInfo : null, null,
new[] { iChromData == iChromDataPrimary }, null, 0, false, false, null, 0,
color, Settings.Default.ChromatogramFontSize, 1);
LineItem curve = (LineItem)_graphHelper.AddChromatogram(PaneKey.DEFAULT, graphItem);
if (matchingTransition == null)
{
curve.Label.Text = label;
}
curve.Line.Width = Settings.Default.ChromatogramLineWidth;
if (null != transition)
{
if (IonMatches(transition.Transition, chromData))
{
color = ChromGraphItem.ColorSelected;
}
}
curve.Color = color;
}
graphPane.Title.IsVisible = false;
graphPane.Legend.IsVisible = true;
_graphHelper.FinishedAddingChromatograms(chromatogramData.StartTime, chromatogramData.EndTime, false);
graphControl.Refresh();
}
graphControl.IsEnableVPan = graphControl.IsEnableVZoom =
!Settings.Default.LockYAxis;
available = true;
}
}
}
catch (Exception)
{
_graphHelper.SetErrorGraphItem(new NoDataMSGraphItem(
Resources.GraphSpectrum_UpdateUI_Failure_loading_spectrum__Library_may_be_corrupted));
return;
}
}
// Show unavailable message, if no spectrum loaded
if (!available)
{
UpdateToolbar();
_nodeGroup = null;
_graphHelper.SetErrorGraphItem(new UnavailableMSGraphItem());
}
}