public void DotpTest()
{
{
var stat1 = new Statistics(new[] { 1.0, 2.0, 3.0 });
Assert.AreEqual(1.0, stat1.Angle(stat1));
Assert.AreEqual(1.0, stat1.AngleSqrt(stat1));
Assert.AreEqual(1.0, stat1.AngleUnitVector(stat1));
Assert.AreEqual(1.0, stat1.NormalizedContrastAngleSqrt(stat1));
// Dot-product of zero should yield zero cos(angle)
var stat2 = new Statistics(new[] { -3.0, 3.0, -1.0 });
Assert.AreEqual(0.0, stat1.Angle(stat2));
Assert.AreEqual(double.NaN, stat1.AngleSqrt(stat2));
Assert.AreEqual(0.0, stat1.AngleUnitVector(stat2));
// Without negatives this is only possible with vectors containing zeros
var statZeros1 = new Statistics(new[] { 1.0, 0.0, 2.0, 0.0, 3.0, 0.0 });
var statZeros2 = new Statistics(new[] { 0.0, 1.0, 0.0, 1.0, 0.0, 3.0 });
Assert.AreEqual(0.0, statZeros1.Angle(statZeros2));
// And this should work for square rooted angle
Assert.AreEqual(0.0, statZeros1.AngleSqrt(statZeros2));
Assert.AreEqual(0.0, statZeros1.AngleUnitVector(statZeros2));
Assert.AreEqual(0.0, statZeros1.NormalizedContrastAngleSqrt(statZeros2));
}
{
var stat0 = new Statistics(new[] { 0.0, 10.0 });
var stat1 = new Statistics(new[] { 0.1, 10.0 });
var stat2 = new Statistics(new[] { 1.0, 10.0 });
var stat3 = new Statistics(new[] { 2.0, 10.0 });
var stat4 = new Statistics(new[] { 5.0, 10.0 });
var stat5 = new Statistics(new[] { 10.0, 10.0 });
double a1 = stat0.Angle(stat1);
double aN1 = stat0.NormalizedContrastAngle(stat1);
Assert.AreEqual(1.0, a1, 0.01);
Assert.AreEqual(0.99, aN1, 0.01);
Assert.AreEqual(a1, Statistics.NormalizedContrastAngleToAngle(aN1), 0.0001);
Assert.AreEqual(aN1, Statistics.AngleToNormalizedContrastAngle(a1), 0.0001);
double a2 = stat0.Angle(stat2);
double aN2 = stat0.NormalizedContrastAngle(stat2);
Assert.AreEqual(0.99, a2, 0.01);
Assert.AreEqual(0.94, aN2, 0.01);
Assert.AreEqual(a2, Statistics.NormalizedContrastAngleToAngle(aN2), 0.0001);
Assert.AreEqual(aN2, Statistics.AngleToNormalizedContrastAngle(a2), 0.0001);
double a3 = stat0.Angle(stat3);
double aN3 = stat0.NormalizedContrastAngle(stat3);
Assert.AreEqual(0.98, a3, 0.01);
Assert.AreEqual(0.87, aN3, 0.01);
Assert.AreEqual(a3, Statistics.NormalizedContrastAngleToAngle(aN3), 0.0001);
Assert.AreEqual(aN3, Statistics.AngleToNormalizedContrastAngle(a3), 0.0001);
double a4 = stat0.Angle(stat4);
double aN4 = stat0.NormalizedContrastAngle(stat4);
Assert.AreEqual(0.89, a4, 0.01);
Assert.AreEqual(0.7, aN4, 0.01);
Assert.AreEqual(a4, Statistics.NormalizedContrastAngleToAngle(aN4), 0.0001);
Assert.AreEqual(aN4, Statistics.AngleToNormalizedContrastAngle(a4), 0.0001);
double a5 = stat0.Angle(stat5);
double aN5 = stat0.NormalizedContrastAngle(stat5);
Assert.AreEqual(0.7, a5, 0.01);
Assert.AreEqual(0.5, aN5, 0.01);
Assert.AreEqual(a5, Statistics.NormalizedContrastAngleToAngle(aN5), 0.0001);
Assert.AreEqual(aN5, Statistics.AngleToNormalizedContrastAngle(a5), 0.0001);
}
}
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));
}
}
