public static List <Feature> GetAllFeaturesFromDatabase(SQLiteConnection conn)
{
List <Feature> returnFeatures = new List <Feature>();
var queryText =
"SELECT s.mz, s.ApexRT, s.ApexIntensity, s.ID_Number, s.SmoothFeatureString, s.RawFeatureString FROM featureTable s";
var queryCommand = new SQLiteCommand(queryText, conn);
var reader = queryCommand.ExecuteReader();
while (reader.Read())
{
var apexRT = double.Parse(reader["ApexRT"].ToString());
var mz = double.Parse(reader["mz"].ToString());
var id = int.Parse(reader["ID_Number"].ToString());
var smoothString = reader["SmoothFeatureString"].ToString();
var rawString = reader["RawFeatureString"].ToString();
List <RTPeak> smoothPeaks = ConvertFeatureStringToPeakList(smoothString);
List <RTPeak> rawPeaks = ConvertFeatureStringToPeakList(rawString);
var feat = new Feature();
feat.ApexTime = apexRT;
feat.AverageMZ = mz;
feat.ID_Number = id;
foreach (var peak in rawPeaks)
{
feat.AddPeak(peak);
}
foreach (var peak in smoothPeaks)
{
feat.AddSmoothPeak(peak);
}
returnFeatures.Add(feat);
//feat.ApexTime = apexRT;
feat.AverageMZ = mz;
}
return(returnFeatures);
}
private void MatchPeaks(List <Feature> features, MZPeak[] currentPeaks, double ppmTolerance, double rt, bool allowMultipleFeatureMatches = false)
{
if (features == null || currentPeaks == null)
{
return;
}
int fCount = features.Count;
if (fCount == 0)
{
features.AddRange(currentPeaks.Select(p => new Feature(p, rt)));
return;
}
int cCount = currentPeaks.Length;
if (cCount == 0)
{
return;
}
int c = 0;
int f = 0;
Feature feature = features[f];
double featureMZ = feature.AverageMZ;
MZPeak cPeak = currentPeaks[c];
ppmTolerance /= 2e6;
double tolerance = cPeak.MZ * ppmTolerance;
double lowmz = cPeak.MZ - tolerance;
List <Feature> featuresToAdd = new List <Feature>(cCount);
while (true)
{
if (featureMZ < lowmz)
{
if (++f == fCount) // Feature mz is to small, go to the next one
{
break; // no more features, so just break out now
}
feature = features[f];
featureMZ = feature.AverageMZ;
continue; // keep the current peak, so continue the loop right away
}
if (featureMZ < cPeak.MZ + tolerance)
{
feature.AddPeak(cPeak, rt); // Peak matches feature, add it to the feature
if (!allowMultipleFeatureMatches)
{
if (++f == fCount) // Feature mz is to small, go to the next one
{
break; // no more features, so just break out now
}
feature = features[f];
featureMZ = feature.AverageMZ;
}
}
else
{
// Peak didn't match any features, so save this peak to start a new feature
featuresToAdd.Add(new Feature(cPeak, rt));
}
if (++c == cCount)
{
break; // no more current peaks, so just break out now
}
cPeak = currentPeaks[c];
tolerance = cPeak.MZ * ppmTolerance;
lowmz = cPeak.MZ - tolerance;
}
// Append unmatched peaks as new features
features.AddRange(featuresToAdd);
// Add left over peaks as new features
while (c < cCount)
{
features.Add(new Feature(currentPeaks[c++], rt));
}
}
