public CurveItem AddChromatogram(PaneKey paneKey, ChromGraphItem chromGraphItem)
{
var chromDisplayState = (ChromDisplayState)_displayState;
chromDisplayState.ChromGraphItems.Add(new KeyValuePair <PaneKey, ChromGraphItem>(paneKey, chromGraphItem));
return(GraphControl.AddGraphItem(chromDisplayState.GetOrCreateGraphPane(GraphControl, paneKey), chromGraphItem, false));
}
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 MassErrorGraphData(SrmDocument document,
IdentityPath identityPath,
DisplayTypeChrom displayType,
ReplicateGroupOp replicateGroupOp,
PaneKey paneKey)
: base(document, identityPath, displayType, replicateGroupOp, paneKey)
{
}
protected GraphData(SrmDocument document, DocNode docNode, DisplayTypeChrom displayType, GraphValues.ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
{
_document = document;
_docNode = docNode;
_displayType = displayType;
ReplicateGroupOp = replicateGroupOp;
_paneKey = paneKey;
}
public AreaGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int?result,
DisplayTypeChrom displayType,
PaneKey paneKey)
: base(document, selectedGroup, selectedProtein, result, displayType, null, paneKey)
{
}
public AreaGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int? result,
DisplayTypeChrom displayType,
PaneKey paneKey)
: base(document, selectedGroup, selectedProtein, result, displayType, null, paneKey)
{
}
protected GraphData(SrmDocument document, IEnumerable <IdentityPath> selectedDocNodePaths, DisplayTypeChrom displayType,
ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
{
_document = document;
_selectedDocNodePaths = ImmutableList.ValueOf(selectedDocNodePaths);
_displayType = displayType;
ReplicateGroupOp = replicateGroupOp;
_paneKey = paneKey;
}
public static void ClickChromatogram(double x, double y, PaneKey? paneKey = null)
{
var graphChromatogram = SkylineWindow.GraphChromatograms.First();
RunUI(() =>
{
graphChromatogram.TestMouseMove(x, y, paneKey);
graphChromatogram.TestMouseDown(x, y, paneKey);
});
WaitForGraphs();
CheckFullScanSelection(x, y, paneKey);
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle = Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide;
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += " (" + paneKey.IsotopeLabelType + ")"; // Not L10N
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle = Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide;
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += @" (" + paneKey.IsotopeLabelType + @")";
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
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);
}
protected SummaryPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
string xAxisTitle =
Helpers.PeptideToMoleculeTextMapper.Translate(Resources.SummaryPeptideGraphPane_SummaryPeptideGraphPane_Peptide,
graphSummary.DocumentUIContainer.DocumentUI.DocumentType);
if (null != paneKey.IsotopeLabelType && !paneKey.IsotopeLabelType.IsLight)
{
xAxisTitle += @" (" + paneKey.IsotopeLabelType + @")";
}
XAxis.Title.Text = xAxisTitle;
XAxis.Type = AxisType.Text;
}
public AreaGraphData(SrmDocument document,
DocNode docNode,
DisplayTypeChrom displayType,
GraphValues.ReplicateGroupOp replicateGroupOp,
int ratioIndex,
AreaNormalizeToData normalize,
AreaExpectedValue expectedVisible,
PaneKey paneKey)
: base(document, docNode, displayType, replicateGroupOp, paneKey)
{
_docNode = docNode;
_ratioIndex = ratioIndex;
_normalize = normalize;
_expectedVisible = expectedVisible;
}
public MSGraphPane GetGraphPane(PaneKey paneKey)
{
return(_displayState.GetGraphPane(GraphControl, paneKey));
}
public static void CheckFullScanSelection(double x, double y, PaneKey? paneKey = null)
{
var graphChromatogram = SkylineWindow.GraphChromatograms.First();
WaitForConditionUI(() => SkylineWindow.GraphFullScan != null && SkylineWindow.GraphFullScan.IsLoaded);
Assert.IsTrue(graphChromatogram.TestFullScanSelection(x, y, paneKey));
}
public AreaReplicateGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
}
// ReSharper disable PossibleMultipleEnumeration
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int?iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List <Tuple <string, bool> >();
foreach (var nodePep in document.Molecules)
{
sequences.Add(new Tuple <string, bool>(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic));
}
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary <IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
{
dictTypeToSet.Add(labelType, pointListCount++);
}
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List <GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
{
continue;
}
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
{
listPoints.Sort(ComparePeptideTimes);
}
else
{
listPoints.Sort(CompareGroupTimes);
}
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
else if (peptideOrder == SummaryPeptideOrder.mass_error)
{
listPoints.Sort(CompareGroupMassErrors);
}
// Init calculated values
var pointPairLists = new List <PointPairList>();
var labels = new List <string>();
var xscalePaths = new List <IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
{
pointPairLists.Add(new PointPairList());
}
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0;
var chargeCurrent = Adduct.EMPTY;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = Adduct.EMPTY;
}
bool addLabel = !displayTotals;
if (displayTotals && !Equals(nodeGroup.TransitionGroup.PrecursorAdduct, chargeCurrent))
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorAdduct;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorAdduct)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
{
label += transitionGroup.LabelTypeText;
}
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(@" ({0:F01})", displayTotals ?
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int?resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest != -1)
{
resultIndex = iBest;
}
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
{
MinY = minY;
}
}
public AreaPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary, paneKey)
{
}
public AreaReplicateGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
}
protected GraphData(SrmDocument document, IdentityPath identityPath, DisplayTypeChrom displayType, ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
: this(document, new[] { identityPath }, displayType, replicateGroupOp, paneKey)
{
}
public SummaryGraphPane CreateReplicatePane(PaneKey key)
{
return(new AreaReplicateGraphPane(GraphSummary, key));
}
public PointF TransformCoordinates(double x, double y, PaneKey? paneKey, CoordType coordType = CoordType.AxisXYScale)
{
var graphPane = _graphHelper.GetGraphPane(paneKey ?? PaneKey.DEFAULT);
return graphPane.GeneralTransform(new PointF((float)x, (float)y), coordType);
}
public void TestMouseMove(double x, double y, PaneKey? paneKey)
{
var mouse = TransformCoordinates(x, y, paneKey);
HandleMouseMove(new MouseEventArgs(MouseButtons.None, 0, (int)mouse.X, (int)mouse.Y, 0));
}
public void TestMouseDown(double x, double y, PaneKey? paneKey)
{
var mouse = TransformCoordinates(x, y, paneKey);
graphControl_MouseDownEvent(null, new MouseEventArgs(MouseButtons.Left, 1, (int)mouse.X, (int)mouse.Y, 0));
}
public bool TestFullScanSelection(double x, double y, PaneKey? paneKey)
{
var graphPane = _graphHelper.GetGraphPane(paneKey ?? PaneKey.DEFAULT);
var selectionDot = graphPane.CurveList[FULLSCAN_SELECTED_INDEX];
var mouse = TransformCoordinates(x, y, paneKey);
var dot = TransformCoordinates(selectionDot[0].X, selectionDot[0].Y, paneKey);
if (!selectionDot.IsVisible)
return false;
const int pixelTolerance = 10;
if (Math.Abs(mouse.X - dot.X) > pixelTolerance || Math.Abs(mouse.Y - dot.Y) > pixelTolerance)
return false;
return true;
}
public AreaGraphData(SrmDocument document,
DocNode docNode,
DisplayTypeChrom displayType,
GraphValues.ReplicateGroupOp replicateGroupOp,
int ratioIndex,
AreaNormalizeToData normalize,
AreaExpectedValue expectedVisible,
PaneKey paneKey)
: base(document, docNode, displayType, replicateGroupOp, paneKey)
{
_docNode = docNode;
_ratioIndex = ratioIndex;
_normalize = normalize;
_expectedVisible = expectedVisible;
}
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 MSGraphPane GetGraphPane(PaneKey paneKey)
{
return _displayState.GetGraphPane(GraphControl, paneKey);
}
public MassErrorPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary, paneKey)
{
}
public AreaPeptideGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary, paneKey)
{
}
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 MassErrorReplicateGraphPane(GraphSummary graphSummary, PaneKey paneKey)
: base(graphSummary)
{
PaneKey = paneKey;
}
private void DisplayTotals(IRegressionFunction timeRegressionFunction,
ChromatogramSet chromatograms,
float mzMatchTolerance,
int countLabelTypes,
ref double bestStartTime,
ref double bestEndTime)
{
// Construct and add graph items for all relevant transition groups.
float fontSize = FontSize;
int lineWidth = LineWidth;
int iCharge = -1;
int? charge = null;
var chromGroupInfos = ChromGroupInfos;
for (int i = 0; i < _nodeGroups.Length; i++)
{
var nodeGroup = _nodeGroups[i];
var chromGroupInfo = chromGroupInfos[i];
if (chromGroupInfo == null)
continue;
ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo);
// Collect the chromatogram info for the transition children
// of this transition group.
ChromatogramInfo infoPrimary = null;
TransitionChromInfo tranPeakInfo = null;
float maxPeakHeight = float.MinValue;
var listChromInfo = new List<ChromatogramInfo>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
var info = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance);
if (info == null)
continue;
listChromInfo.Add(info);
// Keep track of which chromatogram owns the tallest member of
// the peak on the document tree.
var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0);
if (transitionChromInfo == null)
continue;
if (transitionChromInfo.Height > maxPeakHeight)
{
maxPeakHeight = transitionChromInfo.Height;
tranPeakInfo = transitionChromInfo;
infoPrimary = info;
}
// Adjust best peak window used to zoom the graph to the best peak
AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime);
}
// If any transitions are present for this group, add a graph item to
// the graph for it.
if (listChromInfo.Count > 0)
{
if (infoPrimary == null)
infoPrimary = listChromInfo[0];
// Sum the intensities of all transitions into the first chromatogram
infoPrimary.SumIntensities(listChromInfo);
// Apply any transform the user has chosen
infoPrimary.Transform(Transform);
int iColor = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
Color color = COLORS_GROUPS[iColor % COLORS_GROUPS.Length];
bool[] annotateAll = new bool[infoPrimary.NumPeaks];
for (int j = 0; j < annotateAll.Length; j++)
{
var peak = infoPrimary.GetPeak(j);
if (peak.IsForcedIntegration)
continue;
// Exclude any peaks between the boundaries of the chosen peak.
if (tranPeakInfo != null &&
tranPeakInfo.StartRetentionTime < peak.RetentionTime &&
peak.RetentionTime < tranPeakInfo.EndRetentionTime)
continue;
annotateAll[j] = true;
}
var graphItem = new ChromGraphItem(nodeGroup,
null,
infoPrimary,
tranPeakInfo,
timeRegressionFunction,
annotateAll,
null,
0,
false,
false,
0,
color,
fontSize,
lineWidth);
var graphPaneKey = new PaneKey(nodeGroup);
_graphHelper.AddChromatogram(graphPaneKey, graphItem);
}
}
}
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int? iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List<Tuple<string, bool>>();
foreach (var nodePep in document.Molecules)
sequences.Add(new Tuple<string, bool>(nodePep.RawTextId, nodePep.IsProteomic));
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary<IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
dictTypeToSet.Add(labelType, pointListCount++);
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List<GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
continue;
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
listPoints.Sort(ComparePeptideTimes);
else
listPoints.Sort(CompareGroupTimes);
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
// Init calculated values
var pointPairLists = new List<PointPairList>();
var labels = new List<string>();
var xscalePaths = new List<IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
pointPairLists.Add(new PointPairList());
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0, chargeCurrent = 0;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = 0;
}
bool addLabel = !displayTotals;
if (displayTotals && nodeGroup.TransitionGroup.PrecursorCharge != chargeCurrent)
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorCharge;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.RawTextId, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorCharge)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
label += transitionGroup.LabelTypeText;
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(" ({0:F01})", displayTotals ? // Not L10N
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int? resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest !=-1)
resultIndex = iBest;
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
MinY = minY;
}
public SummaryGraphPane CreatePeptidePane(PaneKey key)
{
return(new AreaPeptideGraphPane(GraphSummary, key));
}
private void DisplayTransitions(IRegressionFunction timeRegressionFunction,
TransitionDocNode nodeTranSelected,
ChromatogramSet chromatograms,
float mzMatchTolerance,
TransitionGroupDocNode nodeGroup,
ChromatogramGroupInfo chromGroupInfo,
PaneKey graphPaneKey,
DisplayTypeChrom displayType,
ref double bestStartTime,
ref double bestEndTime)
{
var fileId = chromatograms.FindFile(chromGroupInfo);
// Get points for all transitions, and pick maximum peaks.
ChromatogramInfo[] arrayChromInfo;
var displayTrans = GetDisplayTransitions(nodeGroup, displayType).ToArray();
int numTrans = displayTrans.Length;
int numSteps = 0;
bool allowEmpty = false;
if (IsSingleTransitionDisplay && nodeTranSelected != null)
{
if (!displayTrans.Contains(nodeTranSelected))
{
arrayChromInfo = new ChromatogramInfo[0];
displayTrans = new TransitionDocNode[0];
numTrans = 0;
}
else
{
arrayChromInfo = chromGroupInfo.GetAllTransitionInfo((float) nodeTranSelected.Mz,
mzMatchTolerance,
chromatograms.OptimizationFunction);
if (chromatograms.OptimizationFunction != null)
{
// Make sure the number of steps matches what will show up in the summary
// graphs, or the colors won't match up.
int numStepsExpected = chromatograms.OptimizationFunction.StepCount*2 + 1;
if (arrayChromInfo.Length != numStepsExpected)
{
arrayChromInfo = ResizeArrayChromInfo(arrayChromInfo, numStepsExpected);
allowEmpty = true;
}
}
numTrans = arrayChromInfo.Length;
displayTrans = new TransitionDocNode[numTrans];
for (int i = 0; i < numTrans; i++)
displayTrans[i] = nodeTranSelected;
}
numSteps = numTrans/2;
}
else
{
arrayChromInfo = new ChromatogramInfo[numTrans];
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
// Get chromatogram info for this transition
arrayChromInfo[i] = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance);
}
}
int bestPeakTran = -1;
TransitionChromInfo tranPeakInfo = null;
float maxPeakHeight = float.MinValue;
int numPeaks = chromGroupInfo.NumPeaks;
var maxPeakTrans = new int[numPeaks];
var maxPeakHeights = new float[numPeaks];
for (int i = 0; i < numPeaks; i++)
maxPeakHeights[i] = float.MinValue;
var transform = Transform;
// Prepare arrays of values for library dot-product
double[] expectedIntensities = null;
double[][] peakAreas = null;
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = DocumentUI.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if ((isFullScanMs && !isShowingMsMs && nodeGroup.HasIsotopeDist) ||
(!isFullScanMs && nodeGroup.HasLibInfo))
{
expectedIntensities = new double[numTrans];
peakAreas = new double[numPeaks][];
for (int i = 0; i < numPeaks; i++)
peakAreas[i] = new double[numTrans];
}
// Find the transition with the maximum peak height for the best peak
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
int step = (numSteps > 0 ? i - numSteps : 0);
var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, step);
if (transitionChromInfo == null)
continue;
if (maxPeakHeight < transitionChromInfo.Height)
{
maxPeakHeight = transitionChromInfo.Height;
bestPeakTran = i;
tranPeakInfo = transitionChromInfo;
}
AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime);
}
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
// Store library intensities for dot-product
if (expectedIntensities != null)
{
if (isFullScanMs)
expectedIntensities[i] = nodeTran.HasDistInfo ? nodeTran.IsotopeDistInfo.Proportion : 0;
else
expectedIntensities[i] = nodeTran.HasLibInfo ? nodeTran.LibInfo.Intensity : 0;
}
var info = arrayChromInfo[i];
if (info == null)
continue;
// Apply any active transform
info.Transform(transform);
for (int j = 0; j < numPeaks; j++)
{
var peak = info.GetPeak(j);
// Exclude any peaks between the boundaries of the chosen peak.
if (IntersectPeaks(peak, tranPeakInfo))
continue;
// Store peak intensity for dot-product
if (peakAreas != null)
peakAreas[j][i] = peak.Area;
// Keep track of which transition has the max height for each peak
if (maxPeakHeights[j] < peak.Height)
{
maxPeakHeights[j] = peak.Height;
maxPeakTrans[j] = i;
}
}
}
// Calculate library dot-products, if possible
double[] dotProducts = null;
double bestProduct = 0;
int minProductTrans = isFullScanMs
? TransitionGroupDocNode.MIN_DOT_PRODUCT_MS1_TRANSITIONS
: TransitionGroupDocNode.MIN_DOT_PRODUCT_TRANSITIONS;
if (peakAreas != null && numTrans >= minProductTrans)
{
var tranGroupChromInfo = GetTransitionGroupChromInfo(nodeGroup, fileId, _chromIndex);
double? dotProduct = null;
if (tranGroupChromInfo != null)
{
dotProduct = isFullScanMs
? tranGroupChromInfo.IsotopeDotProduct
: tranGroupChromInfo.LibraryDotProduct;
}
if (dotProduct.HasValue)
{
bestProduct = dotProduct.Value;
var statExpectedIntensities = new Statistics(expectedIntensities);
for (int i = 0; i < peakAreas.Length; i++)
{
var statPeakAreas = new Statistics(peakAreas[i]);
double dotProductCurrent = statPeakAreas.NormalizedContrastAngleSqrt(statExpectedIntensities);
// Only show products that are greater than the best peak product,
// and by enough to be a significant improvement. Also the library product
// on the group node is stored as a float, which means the version
// hear calculated as a double can be larger, but really represent
// the same number.
if (dotProductCurrent > bestProduct &&
dotProductCurrent > 0.5 &&
dotProductCurrent - bestProduct > 0.05)
{
if (dotProducts == null)
dotProducts = new double[numPeaks];
dotProducts[i] = dotProductCurrent;
}
}
}
}
// Create graph items
int iColor = 0;
int lineWidth = LineWidth;
float fontSize = FontSize;
// We want the product ion colors to stay the same whether they are displayed:
// 1. In a single pane with the precursor ions (Transitions -> All)
// 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph)
// 3. In a single pane by themselves (Transition -> Products)
// We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors.
var nodeDisplayType = GetDisplayType(DocumentUI, nodeGroup);
int colorOffset = 0;
if(displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && chromatograms.OptimizationFunction == null)))
{
colorOffset = GetDisplayTransitions(nodeGroup, DisplayTypeChrom.precursors).Count();
}
for (int i = 0; i < numTrans; i++)
{
var info = arrayChromInfo[i];
if (info == null && !allowEmpty)
continue;
var nodeTran = displayTrans[i];
int step = numSteps != 0 ? i - numSteps : 0;
Color color;
bool shade = false;
int width = lineWidth;
if ((numSteps == 0 && ReferenceEquals(nodeTran, nodeTranSelected) ||
(numSteps > 0 && step == 0)))
{
color = ChromGraphItem.ColorSelected;
shade = true;
width++;
}
else
{
color = COLORS_LIBRARY[(iColor + colorOffset) % COLORS_LIBRARY.Length];
}
TransitionChromInfo tranPeakInfoGraph = null;
if (bestPeakTran == i)
tranPeakInfoGraph = tranPeakInfo;
var scanName = nodeTran.FragmentIonName;
if (nodeTran.Transition.Charge != 1) // Positive singly charged is uninteresting
scanName += Transition.GetChargeIndicator(nodeTran.Transition.Charge);
if (nodeTran.Transition.MassIndex != 0)
scanName += Environment.NewLine + Transition.GetMassIndexText(nodeTran.Transition.MassIndex);
var fullScanInfo = new FullScanInfo
{
ChromInfo = info,
ScanName = scanName
};
if (fullScanInfo.ChromInfo != null && fullScanInfo.ChromInfo.ExtractionWidth > 0)
_enableTrackingDot = true;
var graphItem = new ChromGraphItem(nodeGroup,
nodeTran,
info,
tranPeakInfoGraph,
timeRegressionFunction,
GetAnnotationFlags(i, maxPeakTrans, maxPeakHeights),
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
color,
fontSize,
width,
fullScanInfo);
_graphHelper.AddChromatogram(graphPaneKey, graphItem);
if (shade)
{
ShadeGraph(tranPeakInfo,info,timeRegressionFunction,dotProducts,bestProduct,isFullScanMs,step,fontSize,width,fullScanInfo,graphPaneKey);
}
iColor++;
}
var graphPane = _graphHelper.GetGraphPane(graphPaneKey);
if (graphPane == null)
_enableTrackingDot = false;
if (_enableTrackingDot)
{
graphPane.CurveList.Insert(FULLSCAN_TRACKING_INDEX, CreateScanPoint(Color.Black));
graphPane.CurveList.Insert(FULLSCAN_SELECTED_INDEX, CreateScanPoint(Color.Red));
}
}
private void ShadeGraph(TransitionChromInfo tranPeakInfo, ChromatogramInfo info,
IRegressionFunction timeRegressionFunction, double[] dotProducts, double bestProduct, bool isFullScanMs,
int step, float fontSize, int width, FullScanInfo fullScanInfo, PaneKey graphPaneKey)
{
if (tranPeakInfo == null)
return; // Nothing to shade
float end = tranPeakInfo.EndRetentionTime;
float start = tranPeakInfo.StartRetentionTime;
double[] allTimes;
double[] allIntensities;
info.AsArrays(out allTimes, out allIntensities);
var peakTimes = new List<float>();
var peakIntensities = new List<float>();
for (int j = 0; j < allTimes.Length; j++)
{
if (start > allTimes[j])
continue;
if (end < allTimes[j])
break;
peakTimes.Add((float) allTimes[j]);
peakIntensities.Add((float) allIntensities[j]);
}
if (peakIntensities.Count == 0)
return;
// Add peak area shading
float[] peakTimesArray = peakTimes.ToArray();
info = new ChromatogramInfo(peakTimesArray, peakIntensities.ToArray());
var peakShadeItem = new ChromGraphItem(null,
null,
info,
null,
timeRegressionFunction,
new bool[info.NumPeaks],
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
ChromGraphItem.ColorSelected,
fontSize,
width,
fullScanInfo);
var peakShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, peakShadeItem);
peakShadeCurveItem.Label.IsVisible = false;
var lineItem = peakShadeCurveItem as LineItem;
if (lineItem != null)
{
const int fillAlpha = 50;
lineItem.Line.Fill = new Fill(Color.FromArgb(fillAlpha, lineItem.Color));
}
// Add peak background shading
float min = Math.Min(peakIntensities.First(), peakIntensities.Last());
info = new ChromatogramInfo(peakTimesArray,
peakIntensities.Select(intensity => Math.Min(intensity, min)).ToArray());
var backgroundShadeItem = new ChromGraphItem(null,
null,
info,
null,
timeRegressionFunction,
new bool[info.NumPeaks],
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
Color.DarkGray,
fontSize,
2,
fullScanInfo);
var backgroundShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, backgroundShadeItem);
backgroundShadeCurveItem.Label.IsVisible = false;
var lineItem2 = backgroundShadeCurveItem as LineItem;
if (lineItem2 != null)
{
const int fillAlpha = 70;
lineItem2.Line.Fill = new Fill(Color.FromArgb(fillAlpha, Color.Black));
}
}
public CurveItem AddChromatogram(PaneKey paneKey, ChromGraphItem chromGraphItem)
{
var chromDisplayState = (ChromDisplayState) _displayState;
chromDisplayState.ChromGraphItems.Add(new KeyValuePair<PaneKey, ChromGraphItem>(paneKey, chromGraphItem));
return GraphControl.AddGraphItem(chromDisplayState.GetOrCreateGraphPane(GraphControl, paneKey), chromGraphItem, false);
}
