public ChromGraphItem(TransitionGroupDocNode transitionGroupNode,
TransitionDocNode transition,
ChromatogramInfo chromatogram,
TransitionChromInfo tranPeakInfo,
IRegressionFunction timeRegressionFunction,
bool[] annotatePeaks,
double[] dotProducts,
double bestProduct,
bool isFullScanMs,
bool isSummary,
RawTimesInfoItem?displayRawTimes,
int step,
Color color,
float fontSize,
int width,
FullScanInfo fullScanInfo = null)
{
TransitionGroupNode = transitionGroupNode;
TransitionNode = transition;
Chromatogram = chromatogram;
TransitionChromInfo = tranPeakInfo;
TimeRegressionFunction = timeRegressionFunction;
Color = color;
FullScanInfo = fullScanInfo;
_step = step;
_fontSpec = CreateFontSpec(color, fontSize);
_width = width;
_dotProducts = dotProducts;
_bestProduct = bestProduct;
_isFullScanMs = isFullScanMs;
_isSummary = isSummary;
_displayRawTimes = displayRawTimes;
_arrayLabelIndexes = new int[annotatePeaks.Length];
if (chromatogram == null)
{
_measuredTimes = new double[0];
_displayTimes = _measuredTimes;
_intensities = new double[0];
}
else
{
// Cache values early to avoid accessing slow enumerators
// which show up under profiling.
Chromatogram.AsArrays(out _measuredTimes, out _intensities);
if (TimeRegressionFunction == null)
{
_displayTimes = _measuredTimes;
}
else
{
_displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray();
}
// Add peak times to hash set for labeling
int iLastStart = 0;
for (int i = 0; i < chromatogram.NumPeaks; i++)
{
int maxIndex = -1;
if (annotatePeaks[i])
{
ChromPeak peak = chromatogram.GetPeak(i);
maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart);
}
_arrayLabelIndexes[i] = maxIndex;
if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex))
{
_annotatedTimes.Add(maxIndex, i);
}
}
// Calculate best peak index
if (tranPeakInfo != null)
{
iLastStart = 0;
_bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart);
}
}
}
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 ChromGraphItem(TransitionGroupDocNode transitionGroupNode,
TransitionDocNode transition,
ChromatogramInfo chromatogram,
TransitionChromInfo tranPeakInfo,
IRegressionFunction timeRegressionFunction,
bool[] annotatePeaks,
double[] dotProducts,
double bestProduct,
bool isFullScanMs,
bool isSummary,
int step,
Color color,
float fontSize,
int width,
FullScanInfo fullScanInfo = null)
{
TransitionGroupNode = transitionGroupNode;
TransitionNode = transition;
Chromatogram = chromatogram;
TransitionChromInfo = tranPeakInfo;
TimeRegressionFunction = timeRegressionFunction;
Color = color;
FullScanInfo = fullScanInfo;
_step = step;
_fontSpec = CreateFontSpec(color, fontSize);
_width = width;
_dotProducts = dotProducts;
_bestProduct = bestProduct;
_isFullScanMs = isFullScanMs;
_isSummary = isSummary;
_arrayLabelIndexes = new int[annotatePeaks.Length];
if (chromatogram == null)
{
_measuredTimes = new double[0];
_displayTimes = _measuredTimes;
_intensities = new double[0];
}
else
{
// Cache values early to avoid accessing slow enumerators
// which show up under profiling.
Chromatogram.AsArrays(out _measuredTimes, out _intensities);
if (TimeRegressionFunction == null)
{
_displayTimes = _measuredTimes;
}
else
{
_displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray();
}
// Add peak times to hash set for labeling
int iLastStart = 0;
for (int i = 0; i < chromatogram.NumPeaks; i++)
{
int maxIndex = -1;
if (annotatePeaks[i])
{
ChromPeak peak = chromatogram.GetPeak(i);
maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart);
}
_arrayLabelIndexes[i] = maxIndex;
if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex))
_annotatedTimes.Add(maxIndex, i);
}
// Calculate best peak index
if (tranPeakInfo != null)
{
iLastStart = 0;
_bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart);
}
}
}
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));
}
}
