public Regression(List <Tuple <double[], double> > data, IRegressionFunction costFunction)
{
this.countInput = data[0].Item1.Length;
this.data = data;
this.costFunction = costFunction;
sigmas = new double[countInput + 1];
}
public RetentionTimeValues Scale(IRegressionFunction regressionFunction)
{
if (null == regressionFunction)
{
return(this);
}
double startRetentionTime = regressionFunction.GetY(StartRetentionTime);
double endRetentionTime = regressionFunction.GetY(EndRetentionTime);
double retentionTime = regressionFunction.GetY(RetentionTime);
double?fwhm;
if (Fwhm.HasValue)
{
double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value / 2);
double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value / 2);
fwhm = t2 - t1;
}
else
{
fwhm = null;
}
return(new RetentionTimeValues
{
RetentionTime = retentionTime,
StartRetentionTime = startRetentionTime,
EndRetentionTime = endRetentionTime,
Fwhm = fwhm,
});
}
public RetentionTimeValues Scale(IRegressionFunction regressionFunction)
{
if (null == regressionFunction)
{
return(this);
}
double startRetentionTime = regressionFunction.GetY(StartRetentionTime);
double endRetentionTime = regressionFunction.GetY(EndRetentionTime);
double retentionTime = regressionFunction.GetY(RetentionTime);
double?fwhm;
if (Fwhm.HasValue)
{
double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value / 2);
double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value / 2);
fwhm = t2 - t1;
}
else
{
fwhm = null;
}
return(ChangeProp(ImClone(this), im =>
{
im.RetentionTime = retentionTime;
im.StartRetentionTime = startRetentionTime;
im.EndRetentionTime = endRetentionTime;
im.Fwhm = fwhm;
}));
}
public bool TryGetRegressionFunction(ChromFileInfoId chromFileInfoId, out IRegressionFunction regressionFunction)
{
if (ReferenceEquals(chromFileInfoId, ChromFileInfo.Id))
{
regressionFunction = null;
return(true);
}
Tuple <ChromatogramSet, ChromFileInfo> chromSetInfo;
if (_chromSetInfos.TryGetValue(chromFileInfoId, out chromSetInfo))
{
var retentionTimeAlignment =
FileRetentionTimeAlignments.RetentionTimeAlignments.Find(chromSetInfo.Item2);
if (null != retentionTimeAlignment)
{
regressionFunction = retentionTimeAlignment.RegressionLine;
return(true);
}
}
regressionFunction = null;
return(false);
}
private static void AddRetentionTimesToDict(IRetentionTimeProvider retentionTimes,
IRegressionFunction regressionLine,
IDictionary <Target, IrtPeptideAverages> dictPeptideAverages,
IEnumerable <DbIrtPeptide> standardPeptideList)
{
var setStandards = new TargetMap <bool>(standardPeptideList.Select(peptide => new KeyValuePair <Target, bool>(peptide.Target, true)));
foreach (var pepTime in retentionTimes.PeptideRetentionTimes.Where(p => !setStandards.ContainsKey(p.PeptideSequence)))
{
var peptideModSeq = pepTime.PeptideSequence;
var timeSource = retentionTimes.GetTimeSource(peptideModSeq);
var irt = regressionLine.GetY(pepTime.RetentionTime);
if (!dictPeptideAverages.TryGetValue(peptideModSeq, out var pepAverage))
{
dictPeptideAverages.Add(peptideModSeq, new IrtPeptideAverages(peptideModSeq, irt, timeSource));
}
else
{
pepAverage.AddIrt(irt);
}
}
}
public bool TryGetRegressionFunction(ChromFileInfoId chromFileInfoId, out IRegressionFunction regressionFunction)
{
regressionFunction = _retentionTimeRegression.GetUnconversion(chromFileInfoId);
return(regressionFunction != null);
}
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 PointPair CalculatePointPair <TChromInfoData>(int iResult, IEnumerable <TChromInfoData> chromInfoDatas, Func <TChromInfoData, RetentionTimeValues?> getRetentionTimeValues)
where TChromInfoData : ChromInfoData
{
var startTimes = new List <double>();
var endTimes = new List <double>();
var retentionTimes = new List <double>();
var fwhms = new List <double>();
foreach (var chromInfoData in chromInfoDatas)
{
var retentionTimeValues = getRetentionTimeValues(chromInfoData).GetValueOrDefault();
IRegressionFunction regressionFunction = null;
if (null != RetentionTimeTransform.RtTransformOp)
{
RetentionTimeTransform.RtTransformOp.TryGetRegressionFunction(chromInfoData.ChromFileInfo.FileId, out regressionFunction);
}
if (regressionFunction == null)
{
startTimes.Add(retentionTimeValues.StartRetentionTime);
endTimes.Add(retentionTimeValues.EndRetentionTime);
retentionTimes.Add(retentionTimeValues.RetentionTime);
fwhms.Add(retentionTimeValues.Fwhm ?? 0);
}
else
{
startTimes.Add(regressionFunction.GetY(retentionTimeValues.StartRetentionTime));
endTimes.Add(regressionFunction.GetY(retentionTimeValues.EndRetentionTime));
retentionTimes.Add(regressionFunction.GetY(retentionTimeValues.RetentionTime));
if (retentionTimeValues.Fwhm.HasValue)
{
fwhms.Add(regressionFunction.GetY(retentionTimeValues.RetentionTime +
retentionTimeValues.Fwhm.Value / 2)
-
regressionFunction.GetY(retentionTimeValues.RetentionTime -
retentionTimeValues.Fwhm.Value / 2));
}
else
{
fwhms.Add(0);
}
}
}
if (RTPeptideValue.All == RTPeptideGraphPane.RTValue)
{
var point = HiLowMiddleErrorBarItem.MakePointPair(iResult,
new Statistics(endTimes).Mean(),
new Statistics(startTimes).Mean(),
new Statistics(retentionTimes).Mean(),
new Statistics(fwhms).Mean());
return(point.IsInvalid ? PointPairMissing(iResult) : point);
}
IEnumerable <double> values;
switch (RTPeptideGraphPane.RTValue)
{
case RTPeptideValue.FWB:
values = startTimes.Select((startTime, index) => endTimes[index] - startTime);
break;
case RTPeptideValue.FWHM:
values = fwhms;
break;
default:
values = retentionTimes;
break;
}
return(RetentionTimeTransform.AggregateOp.MakeBarValue(iResult, values));
}
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 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));
}
}
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 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);
}
}
}
/// <summary>
/// Display summed transitions for multiple selected peptides.
/// </summary>
private void DisplayPeptides(IRegressionFunction timeRegressionFunction,
ChromatogramSet chromatograms,
float mzMatchTolerance,
int countLabelTypes,
IList<PeptideDocNode> peptideDocNodes,
ref double bestStartTime,
ref double bestEndTime,
out double leftPeakWidth,
out double rightPeakWidth)
{
leftPeakWidth = 0;
rightPeakWidth = 0;
// Construct and add graph items for all relevant transition groups.
float fontSize = FontSize;
int lineWidth = LineWidth;
var chromGroupInfos = ChromGroupInfos;
var lookupChromGroupInfoIndex = new Dictionary<int, int>(_nodeGroups.Length);
for (int i = 0; i < _nodeGroups.Length; i++)
lookupChromGroupInfoIndex[_nodeGroups[i].Id.GlobalIndex] = i;
// Generate a unique short identifier for each peptide.
var peptideNames = new Tuple<string,bool>[peptideDocNodes.Count];
for (int i = 0; i < peptideDocNodes.Count; i++)
peptideNames[i] = new Tuple<string,bool>(peptideDocNodes[i].RawTextId, peptideDocNodes[i].IsProteomic);
var uniqueNames = new UniquePrefixGenerator(peptideNames, 3);
var displayPeptides = new List<DisplayPeptide>();
for (int peptideIndex = 0; peptideIndex < peptideDocNodes.Count; peptideIndex++)
{
var peptideDocNode = peptideDocNodes[peptideIndex];
TransitionChromInfo bestPeakInfo = null;
ChromatogramInfo sumInfo = null;
float maxPeakHeight = float.MinValue;
foreach (var precursor in peptideDocNode.TransitionGroups)
{
int indexInfo;
if (!lookupChromGroupInfoIndex.TryGetValue(precursor.Id.GlobalIndex, out indexInfo))
continue;
var chromGroupInfo = chromGroupInfos[indexInfo];
if (chromGroupInfo == null)
continue;
ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo);
foreach (var nodeTran in precursor.Transitions)
{
var info = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance);
if (info == null)
continue;
if (sumInfo == null)
sumInfo = info;
else
{
float[] sumTimes;
float[] sumIntensities;
if (!AddTransitions.Add(
info.Times, info.Intensities, sumInfo.Times, sumInfo.Intensities,
out sumTimes, out sumIntensities))
continue;
sumInfo = new ChromatogramInfo(sumTimes, sumIntensities);
}
// 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;
bestPeakInfo = transitionChromInfo;
}
}
}
if (sumInfo != null && bestPeakInfo != null)
{
displayPeptides.Add(new DisplayPeptide
{
PeptideIndex = peptideIndex,
SumInfo = sumInfo,
BestPeakInfo = bestPeakInfo
});
}
}
// Order the peptides by height of best peak.
displayPeptides = displayPeptides.OrderByDescending(e => e.BestPeakInfo.Height).ToList();
// Display only the top peptides.
int lastPeptideIndex = Math.Min(MaxPeptidesDisplayed, displayPeptides.Count);
var graphItems = new List<ChromGraphItem>();
for (int i = lastPeptideIndex-1; i >= 0; i--) // smallest peaks first for good z-ordering in graph
{
var bestPeakInfo = displayPeptides[i].BestPeakInfo;
var sumInfo = displayPeptides[i].SumInfo;
var peptideDocNode = peptideDocNodes[displayPeptides[i].PeptideIndex];
// Intersect best peak with summed transition.
if (bestPeakInfo != null && sumInfo.Times.Length > 0)
{
float startRetentionTime = Math.Max(bestPeakInfo.StartRetentionTime, sumInfo.Times[0]);
float endRetentionTime = Math.Min(bestPeakInfo.EndRetentionTime, sumInfo.Times[sumInfo.Times.Length - 1]);
if (endRetentionTime > startRetentionTime)
{
if (bestStartTime > startRetentionTime)
{
bestStartTime = startRetentionTime;
leftPeakWidth = endRetentionTime - startRetentionTime;
}
if (bestEndTime < endRetentionTime)
{
bestEndTime = endRetentionTime;
rightPeakWidth = endRetentionTime - startRetentionTime;
}
bestPeakInfo = new TransitionChromInfo(startRetentionTime, endRetentionTime);
}
}
// Get peptide graph color from SequenceTree.
var peptideGraphInfo = _stateProvider.GetPeptideGraphInfo(peptideDocNode);
Color color = peptideGraphInfo.Color;
sumInfo.Transform(Transform);
bool[] annotateAll = new bool[sumInfo.NumPeaks];
ChromGraphItem graphItem = new ChromGraphItem(null,
null,
sumInfo,
bestPeakInfo,
timeRegressionFunction,
annotateAll,
null,
0,
false,
false,
0,
color,
fontSize,
lineWidth)
{
CurveAnnotation = uniqueNames.GetUniquePrefix(peptideDocNode.RawTextId, peptideDocNode.IsProteomic),
IdPath = _groupPaths[displayPeptides[i].PeptideIndex],
GraphInfo = peptideGraphInfo
};
if (peptideGraphInfo.IsSelected)
graphItems.Insert(0, graphItem);
else
graphItems.Add(graphItem);
}
foreach (var graphItem in graphItems)
{
var curveItem = _graphHelper.AddChromatogram(new PaneKey(), graphItem);
// Make the fill color under the curve more opaque if the curve is selected.
var fillAlpha = graphItem.GraphInfo.IsSelected ? 60 : 15;
((LineItem)curveItem).Line.Fill = new Fill(Color.FromArgb(fillAlpha, graphItem.GraphInfo.Color));
}
}
private void DisplayOptimizationTotals(IRegressionFunction timeRegressionFunction,
ChromatogramSet chromatograms,
float mzMatchTolerance,
ref double bestStartTime,
ref double bestEndTime)
{
// Construct and add graph items for all relevant transition groups.
float fontSize = FontSize;
int lineWidth = LineWidth;
int iColor = 0;
// Get the one and only group
var nodeGroup = _nodeGroups[0];
var chromGroupInfo = ChromGroupInfos[0];
ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo);
int numPeaks = chromGroupInfo.NumPeaks;
// Collect the chromatogram info for the transition children
// of this transition group.
var listChromInfoSets = new List<ChromatogramInfo[]>();
var listTranisitionChromInfoSets = new List<TransitionChromInfo[]>();
int totalOptCount = chromatograms.OptimizationFunction.StepCount*2 + 1;
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
var infos = chromGroupInfo.GetAllTransitionInfo((float) nodeTran.Mz, mzMatchTolerance,
chromatograms.OptimizationFunction);
if (infos.Length == 0)
continue;
// Make sure the total number of chrom info entries match the expected
// no matter what, so that chromatogram colors will match up with peak
// area charts.
if (infos.Length != totalOptCount)
infos = ResizeArrayChromInfo(infos, totalOptCount);
listChromInfoSets.Add(infos);
var transitionChromInfos = new TransitionChromInfo[totalOptCount];
int steps = infos.Length/2;
int offset = totalOptCount/2 - steps;
for (int i = 0; i < infos.Length; i++)
{
transitionChromInfos[i + offset] = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, i - steps);
}
listTranisitionChromInfoSets.Add(transitionChromInfos);
}
if (listChromInfoSets.Count == 0 || totalOptCount == 0)
throw new InvalidDataException(Resources.GraphChromatogram_DisplayOptimizationTotals_No_optimization_data_available);
// Enumerate optimization steps, grouping the data into graph data by step
var listGraphData = new List<OptimizationGraphData>();
for (int i = 0; i < listChromInfoSets.Count; i++)
{
var chromInfos = listChromInfoSets[i];
var transitionChromInfos = listTranisitionChromInfoSets[i];
for (int j = 0; j < chromInfos.Length; j++)
{
if (listGraphData.Count <= j)
listGraphData.Add(new OptimizationGraphData(numPeaks));
listGraphData[j].Add(chromInfos[j], transitionChromInfos[j]);
}
}
// Total and transform the data, and compute which optimization
// set has the most intense peak for each peak group.
int bestPeakData = -1;
TransitionChromInfo tranPeakInfo = null;
float maxPeakHeight = float.MinValue;
var maxPeakData = new int[numPeaks];
var maxPeakHeights = new float[numPeaks];
for (int i = 0; i < numPeaks; i++)
maxPeakHeights[i] = float.MinValue;
var transform = Transform;
for (int i = 0; i < listGraphData.Count; i++)
{
var graphData = listGraphData[i];
var infoPrimary = graphData.InfoPrimary;
if (infoPrimary == null)
continue;
// Sum intensities of all transitions in this
// optimization bucket
infoPrimary.SumIntensities(graphData.ChromInfos);
// Apply any transform the user has chosen
infoPrimary.Transform(transform);
for (int j = 0; j < numPeaks; j++)
{
float height = graphData.PeakHeights[j];
if (height > maxPeakHeights[j])
{
maxPeakHeights[j] = height;
maxPeakData[j] = i;
}
}
if (maxPeakHeight < graphData.TotalHeight)
{
maxPeakHeight = graphData.TotalHeight;
bestPeakData = i;
tranPeakInfo = graphData.TransitionInfoPrimary;
}
AddBestPeakTimes(graphData.TransitionInfoPrimary, ref bestStartTime, ref bestEndTime);
}
// Hide all peaks between the best peak extents
if (tranPeakInfo != null)
{
for (int j = 0; j < numPeaks; j++)
{
if (maxPeakHeights[j] == 0)
continue;
var graphData = listGraphData[maxPeakData[j]];
if (graphData.InfoPrimary == null)
continue;
ChromPeak peak = graphData.InfoPrimary.GetPeak(j);
if (peak.IsForcedIntegration)
continue;
if (IntersectPeaks(peak, tranPeakInfo))
maxPeakHeights[j] = 0;
}
}
// Create graph items
int totalSteps = totalOptCount/2;
for (int i = 0; i < listGraphData.Count; i++)
{
var graphData = listGraphData[i];
if (graphData.InfoPrimary != null)
{
int step = i - totalSteps;
int width = lineWidth;
Color color;
if (step == 0)
{
color = ChromGraphItem.ColorSelected;
width++;
}
else if (nodeGroup.HasLibInfo)
color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length];
else
color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length];
// color = COLORS_HEURISTIC[iColor % COLORS_HEURISTIC.Length];
TransitionChromInfo tranPeakInfoGraph = null;
if (bestPeakData == i)
tranPeakInfoGraph = tranPeakInfo;
var graphItem = new ChromGraphItem(nodeGroup,
null,
graphData.InfoPrimary,
tranPeakInfoGraph,
timeRegressionFunction,
GetAnnotationFlags(i, maxPeakData, maxPeakHeights),
null,
0,
false,
false,
step,
color,
fontSize,
width);
_graphHelper.AddChromatogram(PaneKey.PRECURSORS, graphItem);
}
iColor++;
}
}
private void DisplayAllIonsSummary(IRegressionFunction timeRegressionFunction,
TransitionDocNode nodeTranSelected,
ChromatogramSet chromatograms,
ChromExtractor extractor,
ref double bestStartTime,
ref double bestEndTime)
{
if (ChromGroupInfos.Length == 0)
{
return;
}
var chromGroupInfo = ChromGroupInfos[0];
var info = chromGroupInfo.GetTransitionInfo(0, 0);
var fileId = chromatograms.FindFile(chromGroupInfo);
var nodeGroup = _nodeGroups != null ? _nodeGroups[0] : null;
if (nodeGroup == null)
nodeTranSelected = null;
TransitionChromInfo tranPeakInfo = null;
if (nodeGroup != null)
{
float maxPeakHeight = float.MinValue;
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
// 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 (nodeTranSelected != null)
{
if (ReferenceEquals(nodeTran, nodeTranSelected))
tranPeakInfo = transitionChromInfo;
}
else if (transitionChromInfo.Height > maxPeakHeight)
{
maxPeakHeight = transitionChromInfo.Height;
tranPeakInfo = transitionChromInfo;
}
// Adjust best peak window used to zoom the graph to the best peak
AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime);
}
}
// Apply active transform
info.Transform(Transform);
int numPeaks = info.NumPeaks;
var annotationFlags = new bool[numPeaks];
for (int i = 0; i < numPeaks; i++)
{
// Exclude any peaks between the boundaries of the chosen peak.
annotationFlags[i] = !IntersectPeaks(info.GetPeak(i), tranPeakInfo);
}
var graphItem = new ChromGraphItem(nodeGroup,
nodeTranSelected,
info,
tranPeakInfo,
timeRegressionFunction,
annotationFlags,
null,
0,
true,
true,
0,
COLORS_GROUPS[(int)extractor],
FontSize,
LineWidth);
_graphHelper.AddChromatogram(new PaneKey(nodeGroup), graphItem);
}
public RetentionTimeValues Scale(IRegressionFunction regressionFunction)
{
if (null == regressionFunction)
{
return this;
}
double startRetentionTime = regressionFunction.GetY(StartRetentionTime);
double endRetentionTime = regressionFunction.GetY(EndRetentionTime);
double retentionTime = regressionFunction.GetY(RetentionTime);
double? fwhm;
if (Fwhm.HasValue)
{
double t1 = regressionFunction.GetY(RetentionTime - Fwhm.Value/2);
double t2 = regressionFunction.GetY(RetentionTime + Fwhm.Value/2);
fwhm = t2 - t1;
}
else
{
fwhm = null;
}
return new RetentionTimeValues
{
RetentionTime = retentionTime,
StartRetentionTime = startRetentionTime,
EndRetentionTime = endRetentionTime,
Fwhm = fwhm,
};
}
