private void LoadData(string path, FileType fileType)
{
if (fileType == FileType.DeconvolutionTSV)
{
System.IO.StreamReader reader = new System.IO.StreamReader(path);
string line;
int lineNum = 1;
while (reader.Peek() > 0)
{
line = reader.ReadLine();
List <IsotopicEnvelope> envs = new List <IsotopicEnvelope>();
if (lineNum != 1)
{
var parsedLine = line.Split('\t');
var mass = double.Parse(parsedLine[0]);
var apexRt = double.Parse(parsedLine[10]);
var envelopes = parsedLine[17].Split(new string[] { "[", "]" }, StringSplitOptions.RemoveEmptyEntries);
foreach (var envelope in envelopes)
{
var split = envelope.Split(new string[] { "|", "(", ")" }, StringSplitOptions.RemoveEmptyEntries);
int charge = int.Parse(split[0]);
double rt = double.Parse(split[1]);
int scan = int.Parse(split[2]);
List <MassSpectralPeak> peaks = new List <MassSpectralPeak>();
for (int i = 3; i < split.Length; i++)
{
string[] sp = split[i].Split(new string[] { "," }, StringSplitOptions.RemoveEmptyEntries);
MassSpectralPeak peak = new MassSpectralPeak(double.Parse(sp[0]), double.Parse(sp[1]));
peaks.Add(peak);
}
IsotopicEnvelope env = new IsotopicEnvelope(rt, charge, peaks);
envs.Add(env);
}
var gsdf = envs.GroupBy(p => p.charge).Where(v => v.Count() > 1);
if (gsdf.Any())
{
var deconvolutedFeature = new ChromatographicPeak(envs, mass, apexRt);
if (deconvolutedFeature.GetSignalToBaseline() > 2.0)
{
DeconvolutedFeatures.Add(deconvolutedFeature);
}
}
}
lineNum++;
}
reader.Close();
}
else if (fileType == FileType.MetaMorpheusPsmTsv)
{
System.IO.StreamReader reader = new System.IO.StreamReader(path);
string line;
int lineNum = 1;
while (reader.Peek() > 0)
{
line = reader.ReadLine();
List <IsotopicEnvelope> envs = new List <IsotopicEnvelope>();
if (lineNum != 1)
{
var parsedLine = line.Split('\t');
}
}
}
else if (fileType == FileType.RawFile)
{
string ext = System.IO.Path.GetExtension(path).ToUpperInvariant();
if (ext.Equals(".RAW"))
{
rawFile = ThermoStaticData.LoadAllStaticData(path);
}
if (ext.Equals(".MZML"))
{
rawFile = Mzml.LoadAllStaticData(path);
}
else
{
throw new Exception("Cannot read file format: " + ext);
}
}
else
{
throw new Exception("Cannot read file " + path);
}
}
private void DrawChromatogram(ChromatographicPeak peak, Canvas canvas)
{
if (chargeToColor == null)
{
var converter = new BrushConverter();
chargeToColor = new Dictionary <int, SolidColorBrush>();
chargeToColor.Add(0, Brushes.Maroon);
chargeToColor.Add(1, Brushes.DeepPink);
chargeToColor.Add(2, Brushes.Purple);
chargeToColor.Add(3, Brushes.Blue);
chargeToColor.Add(4, Brushes.Green);
chargeToColor.Add(5, Brushes.Gold);
chargeToColor.Add(6, Brushes.Orange);
//chargeToColor.Add(7, Brushes.DarkCyan);
//chargeToColor.Add(8, Brushes.DimGray);
//chargeToColor.Add(9, Brushes.Firebrick);
//chargeToColor.Add(10, Brushes.LimeGreen);
chargeToColor.Add(int.MinValue, Brushes.Black);
}
List <Tuple <double, double> >[] dataPointsForEachCharge = new List <Tuple <double, double> > [peak.isotopicEnvelopes.Max(p => p.charge)];
double xAxisLowerbound = double.MaxValue;
double xAxisUpperbound = 0;
double yAxisLowerbound = 0;
double yAxisUpperbound = 0;
for (int zIndex = 0; zIndex < dataPointsForEachCharge.Length; zIndex++)
{
int z = zIndex + 1;
dataPointsForEachCharge[zIndex] = new List <Tuple <double, double> >();
var g = peak.isotopicEnvelopes.Where(p => p.charge == z).OrderBy(p => p.retentionTime).ToList();
if (g.Any())
{
double rt = g.Min(p => p.retentionTime);
if (rt < xAxisLowerbound)
{
xAxisLowerbound = rt;
}
rt = g.Max(p => p.retentionTime);
if (rt > xAxisUpperbound)
{
xAxisUpperbound = rt;
}
double inten = g.Max(p => p.intensity);
if (inten > yAxisUpperbound)
{
yAxisUpperbound = inten;
}
}
foreach (var env in g)
{
dataPointsForEachCharge[zIndex].Add(new Tuple <double, double>(env.retentionTime, env.intensity));
}
}
canvas.Children.Clear();
if (xAxisUpperbound - xAxisLowerbound == 0)
{
return;
}
double xAxisStep = (xAxisUpperbound - xAxisLowerbound) / 5;
double yAxisStep = (yAxisUpperbound - yAxisLowerbound) / 5;
DrawGraphAxes(canvas, xAxisLowerbound, xAxisUpperbound, xAxisStep, yAxisLowerbound, yAxisUpperbound, yAxisStep, 20, "{0:0.00}", "0.0E0");
int offset = 0;
// Make some data sets.
bool observedSomethingYet = false;
for (int j = 0; j < dataPointsForEachCharge.Length; j++)
{
PointCollection points = new PointCollection();
var dataPoints = dataPointsForEachCharge[j];
if (dataPoints.Any())
{
observedSomethingYet = true;
}
if (observedSomethingYet)
{
for (int i = 0; i < dataPoints.Count; i++)
{
Point p = new Point(dataPoints[i].Item1, dataPoints[i].Item2);
var transformedPoint = WtoD(p);
points.Add(transformedPoint);
}
Polyline polyline = new Polyline();
polyline.StrokeThickness = lineStroke;
SolidColorBrush brushColor;
if (chargeToColor.TryGetValue(j + 1, out brushColor))
{
}
else
{
brushColor = chargeToColor[int.MinValue];
}
polyline.Stroke = brushColor;
polyline.Points = points;
canvas.Children.Add(polyline);
var rectangle = new Rectangle();
rectangle.Stroke = brushColor;
rectangle.Fill = brushColor;
rectangle.Height = 4;
rectangle.Width = 4;
Canvas.SetTop(rectangle, offset + 5);
Canvas.SetLeft(rectangle, canvas.ActualWidth - 45);
TextBlock textBlock = new TextBlock();
textBlock.FontSize = fontSize;
textBlock.Text = "z=" + (j + 1) + "; " + dataPoints.Count;
Canvas.SetTop(textBlock, offset + 1);
Canvas.SetLeft(textBlock, canvas.ActualWidth - 39);
offset += 12;
canvas.Children.Add(rectangle);
canvas.Children.Add(textBlock);
}
}
TextBlock sbr = new TextBlock();
sbr.Text = peak.GetSignalToBaseline().ToString("F1");
Canvas.SetTop(sbr, 0);
Canvas.SetLeft(sbr, 0);
canvas.Children.Add(sbr);
TextBlock peakcount = new TextBlock();
peakcount.Text = DeconvolutedFeatures.Count.ToString();
Canvas.SetTop(peakcount, 20);
Canvas.SetLeft(peakcount, 0);
canvas.Children.Add(peakcount);
}
private void DrawHeatmapThing(ChromatographicPeak peak, Canvas canvas)
{
var allPeaks = peak.isotopicEnvelopes.SelectMany(p => p.peaks).ToList();
List <Tuple <double, int, double> > datapoints = new List <Tuple <double, int, double> >();
double xAxisLowerbound = peak.isotopicEnvelopes.Min(p => p.retentionTime);
double xAxisUpperbound = peak.isotopicEnvelopes.Max(p => p.retentionTime);
double yAxisLowerbound = -1;
double yAxisUpperbound = 20;
double xAxisStep = (xAxisUpperbound - xAxisLowerbound) / 5;
double yAxisStep = 1;
if (xAxisLowerbound == xAxisUpperbound)
{
xAxisLowerbound--;
xAxisUpperbound++;
}
canvas.Children.Clear();
DrawGraphAxes(canvas, xAxisLowerbound, xAxisUpperbound, xAxisStep, yAxisLowerbound, yAxisUpperbound, yAxisStep, 20, "{0:0.00}", "F0");
foreach (var env in peak.isotopicEnvelopes)
{
foreach (var msPeak in env.peaks)
{
double peakMass = ClassExtensions.ToMass(msPeak.mz, env.charge);
int massDiff = (int)Math.Round(peakMass - peak.mass, 0);
datapoints.Add(new Tuple <double, int, double>(env.retentionTime, massDiff, msPeak.intensity / env.charge));
}
}
if (intensityToColor == null)
{
intensityToColor = new Dictionary <double, SolidColorBrush>();
intensityToColor.Add(0.0, Brushes.Blue);
intensityToColor.Add(0.2, Brushes.Violet);
intensityToColor.Add(0.4, Brushes.Green);
intensityToColor.Add(0.6, Brushes.Gold);
intensityToColor.Add(0.8, Brushes.Orange);
intensityToColor.Add(1.0, Brushes.Red);
}
// Make some data sets.
PointCollection points = new PointCollection();
List <Tuple <double, double, double> > xyz = new List <Tuple <double, double, double> >();
var dataGroupedByMassDiff = datapoints.GroupBy(p => p.Item2);
foreach (var massDiff in dataGroupedByMassDiff)
{
var group = massDiff.ToList().GroupBy(v => v.Item1);
foreach (var g in group)
{
var h = g.ToList();
double intensityHere = h.Sum(v => v.Item3);
xyz.Add(new Tuple <double, double, double>(h.First().Item1, h.First().Item2, intensityHere));
}
}
double maxIntensity = xyz.Max(p => p.Item3);
var timepoints = xyz.GroupBy(p => p.Item1).OrderBy(v => v.Key);
double diff = (timepoints.Last().First().Item1 - timepoints.First().First().Item1);
int numtimepoints = timepoints.Count();
Point tick1W = WtoD(new Point(0, 0));
Point tick2W = WtoD(new Point(diff / numtimepoints, 0));
double widthOfHeatmapRectangle = tick2W.X - tick1W.X;
double summedMaxColumn = timepoints.Max(p => p.Sum(v => v.Item3));
foreach (var timepointIsotopes in timepoints)
{
var list = timepointIsotopes.ToList();
double maxOfColumn = list.Max(p => p.Item3);
foreach (var point in timepointIsotopes)
{
Point p = new Point(point.Item1, point.Item2);
var transformedPoint = WtoD(p);
points.Add(transformedPoint);
var rectangle = new Rectangle();
var dfg = GetHeatmapColor(point.Item3 / maxOfColumn);
//double opacity = (byte)(255 * (list.Sum(g => g.Item3) / summedMaxColumn));
SolidColorBrush brush = new SolidColorBrush(Color.FromArgb(255, (byte)dfg.Item1, (byte)dfg.Item2, (byte)dfg.Item3));
rectangle.Stroke = brush;
rectangle.Fill = brush;
rectangle.Height = 4;
rectangle.Width = widthOfHeatmapRectangle;
Canvas.SetLeft(rectangle, transformedPoint.X - rectangle.Width / 2);
Canvas.SetTop(rectangle, transformedPoint.Y - rectangle.Height / 2);
canvas.Children.Add(rectangle);
//TextBlock ratio = new TextBlock();
//ratio.Text = ((point.Item3 / maxOfColumn) * 100).ToString("F0");
//ratio.FontSize = 8;
//Canvas.SetLeft(ratio, transformedPoint.X - rectangle.Width / 2);
//Canvas.SetTop(ratio, transformedPoint.Y - rectangle.Height / 2 - 2);
//canvas.Children.Add(ratio);
}
}
}
