private static Tracks ComputeSpectraTracks(Spectra spectra, DBOptions options, string outputFilename, int missingScan, int centroid, int minPeaks, double valleyFactor, MaxQuant.CentroidPosition centroidMethod)
{
//Trail.RemoveFinished(ref trails, spectra, -1);
double[] centerMassArray;
float[] centerMassErrorArray;
float[] intensityArray;
float[] minTimeArray;
float[] maxTimeArray;
long[] filePosArray;
//TODO Cycle values to optimize missing scans and centroid values
string file = null;
if (options.WriteMaxQuantPeakFile)
{
file = options.OutputFolder + vsCSV.GetFileName_NoExtension(outputFilename) + "_Peaks.txt";
}
MaxQuant.PeakDetection.Detect(file,
missingScan, //*1-2-3-4-5
centroid, //*1-2-3-4-5-6-7-8-9-10
centroidMethod, //*
false, 0, options.precursorMassTolerance.Value, //TODO ensure its always in ppm
minPeaks, //*1-2-3-4-5-6-7-8-9-10
valleyFactor, //*0.1-0.2-0.3-...-3.0
true,
0,
new Trinity.MaxQuant.RawFileWrapper(spectra),
true,
null, out centerMassArray, out centerMassErrorArray, out intensityArray, out minTimeArray, out maxTimeArray, out filePosArray);
Tracks tracks = new Tracks();
for (int i = 0; i < centerMassArray.Length; i++)
{
tracks.AddTrack(centerMassArray[i], (minTimeArray[i] + maxTimeArray[i]) * 0.5, minTimeArray[i], maxTimeArray[i], intensityArray[i]);
}
return(tracks);
}
public static Tracks Import(string filename, DBOptions dbOptions)
{
vsCSV csv = new vsCSV(filename);
if (csv.LINES_LIST.Count == 0 || csv.LINES_LIST[0].CompareTo(Track.TITLE) != 0)
{
return(null);
}
Tracks tracks = new Tracks();
for (int i = 1; i < csv.LINES_LIST.Count; i++)
{
try
{
string[] splits = csv.LINES_LIST[i].Split(vsCSV._Generic_Separator);
tracks.AddTrack(double.Parse(splits[0]), double.Parse(splits[1]), double.Parse(splits[3]), double.Parse(splits[4]), double.Parse(splits[2]));
}
catch (Exception)
{
dbOptions.ConSole.WriteLine("Error parsing line : " + csv.LINES_LIST[i]);
}
}
return(tracks);
}
