public SummaryTransitionGroupPeakData(SrmDocument document,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
ChromatogramSet chromatogramSet,
ChromatogramGroupInfo chromGroupInfoPrimary)
{
_peakIndex = -1;
NodeGroup = nodeGroup;
IsStandard = document.Settings.PeptideSettings.Modifications.InternalStandardTypes
.Contains(nodeGroup.TransitionGroup.LabelType);
TransitionPeakData = Ms1TranstionPeakData = Ms2TranstionPeakData = EMPTY_DATA;
ChromatogramGroupInfo[] arrayChromInfo;
var measuredResults = document.Settings.MeasuredResults;
float mzMatchTolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
if (measuredResults.TryLoadChromatogram(chromatogramSet, nodePep, nodeGroup, mzMatchTolerance, false,
out arrayChromInfo))
{
_chromGroupInfo = arrayChromInfo.FirstOrDefault(ci =>
Equals(ci.FilePath, chromGroupInfoPrimary.FilePath));
if (_chromGroupInfo != null)
{
int ms1Count = 0, ms2Count = 0, totalCount = 0;
// Assume there will be one per transtion
var listPeakData = new ITransitionPeakData <ISummaryPeakData> [nodeGroup.TransitionCount];
foreach (var nodeTran in nodeGroup.Transitions)
{
var tranInfo = _chromGroupInfo.GetTransitionInfo(nodeTran, mzMatchTolerance, chromatogramSet.OptimizationFunction);
if (tranInfo == null)
{
continue;
}
listPeakData[totalCount++] = new SummaryTransitionPeakData(document, nodeTran, chromatogramSet, tranInfo);
if (nodeTran.IsMs1)
{
ms1Count++;
}
else
{
ms2Count++;
}
}
// If something was missing reallocate, which can't be slower than List.ToArray()
if (totalCount < listPeakData.Length)
{
var peakDatasShort = new ITransitionPeakData <ISummaryPeakData> [totalCount];
Array.Copy(listPeakData, peakDatasShort, totalCount);
listPeakData = peakDatasShort;
}
TransitionPeakData = listPeakData.ToArray();
Ms1TranstionPeakData = GetTransitionTypePeakData(ms1Count, ms2Count, true);
Ms2TranstionPeakData = GetTransitionTypePeakData(ms1Count, ms2Count, false);
}
}
}
public SummaryTransitionGroupPeakData(SrmDocument document,
PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
ChromatogramSet chromatogramSet,
ChromatogramGroupInfo chromGroupInfoPrimary)
{
_peakIndex = -1;
NodeGroup = nodeGroup;
IsStandard = document.Settings.PeptideSettings.Modifications.InternalStandardTypes
.Contains(nodeGroup.TransitionGroup.LabelType);
TransitionPeakData = Ms1TranstionPeakData = Ms2TranstionPeakData = EMPTY_DATA;
ChromatogramGroupInfo[] arrayChromInfo;
var measuredResults = document.Settings.MeasuredResults;
float mzMatchTolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
if (measuredResults.TryLoadChromatogram(chromatogramSet, nodePep, nodeGroup, mzMatchTolerance, false,
out arrayChromInfo))
{
_chromGroupInfo = arrayChromInfo.FirstOrDefault(ci =>
Equals(ci.FilePath, chromGroupInfoPrimary.FilePath));
if (_chromGroupInfo != null)
{
int ms1Count = 0, ms2Count = 0;
var listPeakData = new List <ITransitionPeakData <ISummaryPeakData> >();
foreach (var nodeTran in nodeGroup.Transitions)
{
var tranInfo = _chromGroupInfo.GetTransitionInfo(nodeTran.Mz, mzMatchTolerance);
if (tranInfo == null)
{
continue;
}
listPeakData.Add(new SummaryTransitionPeakData(document, nodeTran, chromatogramSet, tranInfo));
if (nodeTran.IsMs1)
{
ms1Count++;
}
else
{
ms2Count++;
}
}
TransitionPeakData = listPeakData.ToArray();
Ms1TranstionPeakData = GetTransitionTypePeakData(ms1Count, ms2Count, true);
Ms2TranstionPeakData = GetTransitionTypePeakData(ms1Count, ms2Count, false);
}
}
}
public IonAbundances(TransitionGroupDocNode nodeTranGroup, ChromatogramGroupInfo chromGroupInfo,
float mzMatchTolerance, int peakIndex) : this()
{
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfoCached = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance);
if (chromInfoCached == null)
{
continue;
}
Add(nodeTran, chromInfoCached.GetPeak(peakIndex).Area);
}
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
private static ChromPeak GetLargestPeak(TransitionGroupDocNode nodeTranGroup,
ChromatogramGroupInfo chromGroupInfo, int peakIndex, float mzMatchTolerance)
{
var largestPeak = ChromPeak.EMPTY;
foreach (var peak in
from transitionDocNode in nodeTranGroup.Transitions
select chromGroupInfo.GetTransitionInfo((float)transitionDocNode.Mz, mzMatchTolerance)
into chromInfo where chromInfo != null
select chromInfo.GetPeak(peakIndex))
{
if (peak.Height > largestPeak.Height)
{
largestPeak = peak;
}
}
return(largestPeak);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color peptideColor, out ChromExtra extra, out TimeIntensities timeIntensities)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
timeIntensities = tranInfo.TimeIntensities;
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
return(true);
}
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 static ChromPeak GetLargestPeak(TransitionGroupDocNode nodeTranGroup,
ChromatogramGroupInfo chromGroupInfo, int peakIndex, float mzMatchTolerance)
{
var largestPeak = ChromPeak.EMPTY;
foreach (var peak in
from transitionDocNode in nodeTranGroup.Transitions
select chromGroupInfo.GetTransitionInfo((float) transitionDocNode.Mz, mzMatchTolerance)
into chromInfo where chromInfo != null
select chromInfo.GetPeak(peakIndex))
{
if (peak.Height > largestPeak.Height)
largestPeak = peak;
}
return largestPeak;
}
public IonAbundances(TransitionGroupDocNode nodeTranGroup, ChromatogramGroupInfo chromGroupInfo,
float mzMatchTolerance, int peakIndex)
: this()
{
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfoCached = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance);
if (chromInfoCached == null)
continue;
Add(nodeTran, chromInfoCached.GetPeak(peakIndex).Area);
}
}