public bool ApexCheck(Feature feature, double startTime, double stopTime)
{
var relevantPeaks = feature.SmoothRTPeaks.Where(x => x.RT <= stopTime && x.RT >= startTime).ToList();
if (relevantPeaks.Count > 0)
{
double startIntensity = relevantPeaks.First().Intensity;
double stopIntensity = relevantPeaks.Last().Intensity;
double maxIntensity = 0;
RTPeak maxPeak = null;
bool valid = false;
foreach (RTPeak peak in relevantPeaks)
{
if (peak.Intensity > startIntensity && peak.Intensity > stopIntensity)
{
valid = true;
if (peak.Intensity > maxIntensity)
{
maxIntensity = peak.Intensity;
maxPeak = peak;
feature.MaxPeak = peak;
}
}
}
return(valid);
}
return(false);
}
public int GetRTPeakIndex(Feature feature, RTPeak peak)
{
int returnIndex = Array.BinarySearch(feature.SmoothRTPeaks.ToArray(), peak);
if (returnIndex < 0)
{
returnIndex = ~returnIndex;
}
return(returnIndex);
}
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 int GetRightStopIndex(int startIndex, List <RTPeak> smoothPeaks, double threshold)
{
if (startIndex + 1 < smoothPeaks.Count)
{
RTPeak previousPeak = smoothPeaks[startIndex];
RTPeak currentpeak = smoothPeaks[startIndex + 1];
if (currentpeak.Intensity > previousPeak.Intensity && currentpeak.Intensity < threshold)
{
return(startIndex);
}
return(GetRightStopIndex(startIndex + 1, smoothPeaks, threshold));
}
return(startIndex);
}
public static List <Feature> GetFeatures(string name, SQLiteConnection conn, double minTime, double maxTime)
{
var queryText = "SELECT s.ID, s.mz, s.Name, s.ApexRT, s.ApexIntensity, s.SmoothFeatureString FROM featureTable s WHERE s.Name=@Name AND s.ApexRT<@Max AND s.ApexRT>@Min";
var queryCommand = new SQLiteCommand(queryText, conn);
queryCommand.Parameters.AddWithValue("@Name", name);
queryCommand.Parameters.AddWithValue("@Min", minTime);
queryCommand.Parameters.AddWithValue("@Max", maxTime);
List <Feature> returnFeatures = new List <Feature>();
var reader = queryCommand.ExecuteReader();
while (reader.Read())
{
var id = reader["ID"].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('|');
//double mz = double.Parse(parts[0]);
//double rt = double.Parse(parts[1]);
string[] peaks = parts[0].Split(';');
var feature = new Feature();
// feature.AverageMZ = mz;
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;
returnFeatures.Add(feature);
}
return(returnFeatures);
}
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 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 int GetLeftStopIndex(int startIndex, List <RTPeak> smoothPeaks, double threshold)
{
if (startIndex - 1 >= 0)
{
RTPeak previousPeak = smoothPeaks[startIndex];
RTPeak currentpeak = smoothPeaks[startIndex - 1];
if (currentpeak.Intensity > previousPeak.Intensity && currentpeak.Intensity < threshold)
{
return(startIndex);
}
return(GetLeftStopIndex(startIndex - 1, smoothPeaks, threshold));
}
else
{
return(startIndex);
}
}
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> GetRollingAveragePeaks(List <RTPeak> peaks, int period)
{
List <RTPeak> outPeaks = new List <RTPeak>();
for (int i = 0; i < peaks.Count; i++)
{
if (i >= period)
{
double total = 0;
for (int x = i; x > (i - period); x--)
{
total += peaks[x].Intensity;
}
double average = total / (double)period;
RTPeak newPeak = new RTPeak(peaks[i].MZ, average, peaks[i - (period / 2)].RT);
outPeaks.Add(newPeak);
}
}
return(outPeaks);
}
public List <Feature> GetApexTimePoints(Feature feature)
{
List <RTPeak> rtPeaks = feature.SmoothRTPeaks;
List <double> apexPoints = new List <double>();
List <int> apexIndexes = new List <int>();
List <Feature> returnFeatures = new List <Feature>();
double peakRise = 1.05;
double peakFall = 0.9;
if (rtPeaks.Count > 0)
{
double intensityLeft = rtPeaks.First().Intensity;
double intensityRight = rtPeaks.Last().Intensity;
double threshold = intensityLeft * 2.5;
if (intensityRight < intensityLeft)
{
threshold = intensityRight * 2.5;
}
bool rising = false;
bool falling = false;
RTPeak holdingMaxPeak = new RTPeak(0, 0, 0);
int holdingMaxIndex = 0;
for (int i = 0; i < rtPeaks.Count - 1; i++)
{
RTPeak currentPoint = rtPeaks[i];
RTPeak nextPoint = rtPeaks[i + 1];
if (!rising && !falling)
{
if (nextPoint.Intensity >= (currentPoint.Intensity * peakRise) && nextPoint.Intensity > threshold)
{
rising = true;
}
}
if (rising)
{
if (nextPoint.Intensity > currentPoint.Intensity)
{
continue;
}
else
{
holdingMaxPeak = currentPoint;
holdingMaxIndex = i;
rising = false;
falling = true;
}
}
if (falling)
{
if (nextPoint.Intensity < holdingMaxPeak.Intensity)
{
if (nextPoint.Intensity < holdingMaxPeak.Intensity * peakFall)
{
apexPoints.Add(holdingMaxPeak.RT);
apexIndexes.Add(holdingMaxIndex);
falling = false;
}
}
else
{
holdingMaxPeak = nextPoint;
holdingMaxIndex = i + 1;
}
}
}
var subFeatures = GetSubFeatures(feature, apexIndexes).ToList();
return(subFeatures);
}
return(null);
}
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));
}
