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);
}
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 IEnumerable <Feature> GetSubFeatures(Feature feature, List <int> apexIndexes)
{
List <Feature> returnList = new List <Feature>();
foreach (int apexIndex in apexIndexes)
{
double threshold = feature.SmoothRTPeaks[apexIndex].Intensity * 0.99;
int leftIndex = GetLeftStopIndex(apexIndex, feature.SmoothRTPeaks, threshold);
int rightIndex = GetRightStopIndex(apexIndex, feature.SmoothRTPeaks, threshold);
Feature newFeature = new Feature();
newFeature.ApexTime = feature.SmoothRTPeaks[apexIndex].RT;
for (int i = leftIndex; i <= rightIndex; i++)
{
newFeature.AddSmoothPeak(feature.SmoothRTPeaks[i]);
}
yield return(newFeature);
}
}