public Feature(MZPeak firstPeak, double RT, double HCDEnergy = 0)
{
this.allRTPeaks = new List <RTPeak>();
this.smoothRTPeaks = new List <RTPeak>();
this.minRT = RT;
this.maxRT = RT;
RTPeak newRTPeak = new RTPeak(firstPeak, RT);
this.allRTPeaks.Add(newRTPeak);
this.maxPeak = newRTPeak;
this.totalMZTimesIntensity += (firstPeak.Intensity * firstPeak.MZ);
this.totalIntensity += (firstPeak.Intensity);
this.averageMZ = firstPeak.MZ;
newRTPeak.HCDEnergy = HCDEnergy;
}
public void AddSmoothPeak(RTPeak peak)
{
this.smoothRTPeaks.Add(peak);
if (this.maxPeak == null)
{
this.maxPeak = peak;
}
if (peak.Intensity > this.maxPeak.Intensity)
{
this.maxPeak = peak;
}
this.totalMZTimesIntensity += (peak.Intensity * peak.MZ);
this.totalIntensity += (peak.Intensity);
this.averageMZ = (this.totalMZTimesIntensity / this.totalIntensity);
}
public void AddPeak(MZPeak peak, double RT, double HCDEnergy = 0)
{
RTPeak newRTPeak = new RTPeak(peak, RT);
this.allRTPeaks.Add(newRTPeak);
if (peak.Intensity > maxPeak.Intensity)
{
apexTime = RT;
maxPeak = newRTPeak;
}
this.maxRT = RT;
this.totalMZTimesIntensity += (peak.Intensity * peak.MZ);
this.totalIntensity += (peak.Intensity);
this.averageMZ = (this.totalMZTimesIntensity / this.totalIntensity);
newRTPeak.HCDEnergy = HCDEnergy;
}
public static List <Feature> GetFeatures(double minTime, double maxTime, SQLiteConnection conn)
{
var queryText =
"SELECT s.mz, s.ApexRT, s.ApexIntensity, s.ID_Number, s.SmoothFeatureString, s.RawFeatureString FROM featureTable s WHERE s.ApexRT>@minTime AND s.ApexRT<@maxTime";
var command = new SQLiteCommand(queryText, conn);
command.Parameters.AddWithValue("@minTime", minTime);
command.Parameters.AddWithValue("@maxtime", maxTime);
List <Feature> returnFeatures = new List <Feature>();
var reader = command.ExecuteReader();
while (reader.Read())
{
var id = int.Parse(reader["ID_Number"].ToString());
double mz = double.Parse(reader["mz"].ToString());
var apexRT = double.Parse(reader["ApexRT"].ToString());
var apexIntensity = double.Parse(reader["ApexIntensity"].ToString());
var featString = reader["SmoothFeatureString"].ToString();
string[] parts = featString.Split('|');
string[] peaks = parts[0].Split(';');
var feature = new Feature();
feature.ApexTime = apexRT;
foreach (var peak in peaks)
{
if (!string.IsNullOrEmpty(peak))
{
string[] peakParts = peak.Split(',');
double time = double.Parse(peakParts[0]);
double intensity = double.Parse(peakParts[1]);
var newPeak = new RTPeak(mz, intensity, time);
feature.AddSmoothPeak(newPeak);
if (Math.Round(newPeak.RT, 3) == Math.Round(apexRT, 3))
{
feature.totalIntensity += newPeak.Intensity;
}
}
}
feature.AverageMZ = mz;
feature.maxIntensity = apexIntensity;
feature.ID_Number = id;
returnFeatures.Add(feature);
}
reader.Close();
reader.Dispose();
command.Dispose();
return(returnFeatures);
}
public void AddPeak(RTPeak peak)
{
this.allRTPeaks.Add(peak);
if (maxPeak == null)
{
MaxPeak = peak;
}
if (peak.Intensity > maxPeak.Intensity)
{
apexTime = peak.RT;
maxPeak = peak;
}
this.maxRT = peak.RT;
this.totalMZTimesIntensity += (peak.Intensity * peak.MZ);
this.totalIntensity += (peak.Intensity);
this.averageMZ = (this.totalMZTimesIntensity / this.totalIntensity);
}
public static List <RTPeak> ConvertFeatureStringToPeakList(string featureString)
{
List <RTPeak> returnList = new List <RTPeak>();
string[] parts = featureString.Split(';');
foreach (var part in parts)
{
if (!string.IsNullOrEmpty(part))
{
string[] subparts = part.Split(',');
double rt = double.Parse(subparts[0]);
double intensity = double.Parse(subparts[1]);
var newRTPeak = new RTPeak();
newRTPeak.RT = rt;
newRTPeak.Intensity = intensity;
returnList.Add(newRTPeak);
}
}
return(returnList);
}
public List <RTPeak> RemoveSolventFrontFromTIC(List <RTPeak> ticChroma, double firstScanTime)
{
//added this line for the sake of MJR
return(ticChroma);
//assume the solvent front comes off and ends within the first four minutes of the run
var timeRange = new DoubleRange(firstScanTime, firstScanTime + 4);
//rank order all tic points by intensity
ticChroma = ticChroma.OrderByDescending(x => x.Intensity).ToList();
//find first tic point that occurs within that first two minutes and store the peak
RTPeak holdPeak = null;
foreach (var peak in ticChroma)
{
if (timeRange.Contains(peak.RT))
{
holdPeak = peak;
break;
}
}
//reorder the tic chromatogram by time
ticChroma = ticChroma.OrderBy(x => x.RT).ToList();
//binary search your way to the solvent front peak you just found
int index = ticChroma.BinarySearch(holdPeak);
int nextIndex = index;
//start riding the curve to the right (increased time)
for (int i = index; i < ticChroma.Count; i++)
{
var currPeak = ticChroma[i];
//once you are at .2 intensity as what you were at the apex start clocking
if (currPeak.Intensity < holdPeak.Intensity * .2)
{
nextIndex = i;
break;
}
}
//keep riding the curve until you hit an point where the intensity increases from the previous point
RTPeak prevPeak = ticChroma[nextIndex];
int lastIndex = nextIndex;
for (int i = nextIndex; i < ticChroma.Count; i++)
{
var currPeak = ticChroma[i];
if (currPeak.Intensity > prevPeak.Intensity)
{
lastIndex = i;
break;
}
else
{
prevPeak = currPeak;
}
}
//every point after that should be free of the solvent front.
ticChroma.RemoveRange(0, lastIndex);
return(ticChroma);
}
public bool Equals(RTPeak obj)
{
return(obj is RTPeak && Equals((RTPeak)obj));
}
public int CompareTo(Object other)
{
RTPeak otherPeak = (RTPeak)other;
return(RT.CompareTo(otherPeak.RT));
}
public int CompareTo(RTPeak other)
{
return(RT.CompareTo(other.RT));
}
