public GraphData(SrmDocument document, int resultIndex, bool bestResult, PointsTypeMassError pointsType)
{
_document = document;
_resultIndex = resultIndex;
_replicateDisplay = ShowReplicate;
var vals = new List <double>();
var dictPpmBin2ToCount = new Dictionary <int, int>();
_displayType = MassErrorGraphController.HistogramDisplayType;
_binSize = Settings.Default.MassErorrHistogramBinSize;
_transition = MassErrorGraphController.HistogramTransiton;
_pointsType = pointsType;
if (document != null)
{
bool decoys = pointsType == PointsTypeMassError.decoys;
bool precursors = _displayType == DisplayTypeMassError.precursors;
foreach (var nodePep in document.Molecules)
{
if (decoys != nodePep.IsDecoy)
{
continue;
}
var replicateIndex = bestResult && nodePep.BestResult != -1 ? nodePep.BestResult : resultIndex;
foreach (var nodeGroup in nodePep.TransitionGroups)
{
foreach (var nodeTran in nodeGroup.Transitions)
{
if (precursors != nodeTran.IsMs1)
{
continue;
}
if (replicateIndex >= 0)
{
AddChromInfo(nodeGroup, nodeTran, replicateIndex, dictPpmBin2ToCount, vals);
}
else
{
for (int i = 0; i < nodeTran.Results.Count; i++)
{
AddChromInfo(nodeGroup, nodeTran, i, dictPpmBin2ToCount, vals);
}
}
}
}
}
}
_bins = dictPpmBin2ToCount.Select(ppmBin => new PpmBinCount((float)(ppmBin.Key * _binSize), ppmBin.Value)).ToArray();
var statVals = new Statistics(vals.ToArray());
_mean = statVals.Mean();
_stdDev = statVals.StdDev();
}
public GraphData(SrmDocument document, GraphData dataPrevious, int resultIndex,
bool bestResult, PointsTypeMassError pointsType)
{
_document = document;
_resultIndex = resultIndex;
_replicateDisplay = ShowReplicate;
int[,] counts2D = EMPTY_COUNTS;
_displayType = MassErrorGraphController.HistogramDisplayType;
_binSizePpm = Settings.Default.MassErorrHistogramBinSize;
_transition = MassErrorGraphController.HistogramTransiton;
_xAxis = MassErrorGraphController.Histogram2DXAxis;
_pointsType = pointsType;
if (_pointsType == PointsTypeMassError.targets_1FDR && !document.Settings.PeptideSettings.Integration.PeakScoringModel.IsTrained)
{
_pointsType = PointsTypeMassError.targets;
}
bool decoys = pointsType == PointsTypeMassError.decoys;
bool precursors = _displayType == DisplayTypeMassError.precursors;
while (ReferenceEquals(counts2D, EMPTY_COUNTS))
{
if (_maxMass != double.MinValue)
{
counts2D = new int[xAxisBins, (int)((_maxMass - _minMass) / _binSizePpm + 1)];
}
foreach (var nodePep in document.Molecules)
{
if (decoys != nodePep.IsDecoy)
{
continue;
}
var replicateIndex = bestResult && nodePep.BestResult != -1 ? nodePep.BestResult : resultIndex;
foreach (var nodeGroup in nodePep.TransitionGroups)
{
foreach (var nodeTran in nodeGroup.Transitions)
{
if (precursors != nodeTran.IsMs1)
{
continue;
}
var mz = nodeTran.Mz.Value;
if (replicateIndex >= 0)
{
AddChromInfo(nodeGroup, nodeTran, replicateIndex, mz, counts2D);
}
else
{
for (int i = 0; i < nodeTran.Results.Count; i++)
{
AddChromInfo(nodeGroup, nodeTran, i, mz, counts2D);
}
}
}
}
}
// No values. Leave _maxCount == 0
if (_maxMass == double.MinValue)
{
return;
}
}
var points = new List <Point3D>();
for (int x = 0; x < counts2D.GetLength(0); x++)
{
for (int y = 0; y < counts2D.GetLength(1); y++)
{
int count = counts2D[x, y];
if (count > 0)
{
double binSizeX = (_maxX - _minX) / xAxisBins;
double xPoint = x * binSizeX + _minX + binSizeX / 2;
double yPoint = y * _binSizePpm + _minMass + _binSizePpm / 2;
points.Add(new Point3D(xPoint, yPoint, count));
}
_maxCount = Math.Max(_maxCount, count);
}
}
_heatMapData = new HeatMapData(points);
}
