public double GetDemoninatorTerm(EISpectrum eiSpec)
{
double returnVal = 0;
foreach (MZPeak peak in eiSpec.FinalNormalizedEIPeaks)
{
returnVal += (peak.MZ * peak.Intensity);
}
return(returnVal);
}
public static void ReadInGCFeat(List <Feature> features, List <FeatureGroup> groups, List <EISpectrum> spectra, out Chromatogram chroma, out string name, SQLiteConnection conn)
{
var queryText = "SELECT s.mz, s.ApexRT, s.ApexIntensity, s.SmoothFeatureString, s.RawFeatureString, s.ID_Number FROM featureTable s";
var queryCommand = new SQLiteCommand(queryText, conn);
var reader = queryCommand.ExecuteReader();
Dictionary <int, Feature> featDict = new Dictionary <int, Feature>();
while (reader.Read())
{
var mz = double.Parse(reader["mz"].ToString());
var apexIntensity = double.Parse(reader["ApexIntensity"].ToString());
var apexRT = double.Parse(reader["ApexRT"].ToString());
var smoothString = reader["SmoothFeatureString"].ToString();
var rawString = reader["RawFeatureString"].ToString();
var idNum = int.Parse(reader["ID_Number"].ToString());
List <RTPeak> rawPeaks = ConvertFeatureStringToPeakList(rawString);
List <RTPeak> smoothPeaks = ConvertFeatureStringToPeakList(smoothString);
var feat = new Feature();
feat.ApexTime = apexRT;
foreach (var peak in rawPeaks)
{
feat.AddPeak(peak);
}
foreach (var peak in smoothPeaks)
{
feat.AddSmoothPeak(peak);
}
feat.AverageMZ = mz;
feat.maxIntensity = apexIntensity;
feat.ID_Number = idNum;
features.Add(feat);
featDict.Add(idNum, feat);
}
reader.Close();
queryText = "SELECT s.ApexRT, s.IncludedFeatures, s.PeakList, s.GroupID FROM featureGroupTable s";
queryCommand = new SQLiteCommand(queryText, conn);
reader = queryCommand.ExecuteReader();
while (reader.Read())
{
var apexRT = double.Parse(reader["ApexRT"].ToString());
var includedString = reader["IncludedFeatures"].ToString();
var peakList = reader["PeakList"].ToString();
var groupID = int.Parse(reader["GroupID"].ToString());
List <MZPeak> peaks = ConvertPeakListString(peakList);
string[] includedFeatures = includedString.Split(';');
var featureGroup = new FeatureGroup();
featureGroup.ApexTime = apexRT;
featureGroup.finalPeaks = peaks;
featureGroup.groupID = groupID;
foreach (var feat in includedFeatures)
{
if (!string.IsNullOrEmpty(feat))
{
int id = int.Parse(feat);
featureGroup.allFeatures.Add(featDict[id]);
}
}
var norm = new Normalization();
var eiSpectrum = new EISpectrum();
eiSpectrum.FinalEIPeaks = peaks;
eiSpectrum.FinalNormalizedEIPeaks = peaks;
eiSpectrum.FeatureGroup = featureGroup;
eiSpectrum.ApexTimeEI = apexRT;
groups.Add(featureGroup);
spectra.Add(eiSpectrum);
}
queryText = "SELECT s.TICChroma, s.Name FROM ticTable s";
queryCommand = new SQLiteCommand(queryText, conn);
reader = queryCommand.ExecuteReader();
List <double> rts = new List <double>();
List <double> intensities = new List <double>();
name = "";
chroma = null;
while (reader.Read())
{
var tic = reader["TICChroma"].ToString();
name = reader["Name"].ToString();
string[] parts = tic.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]);
rts.Add(rt);
intensities.Add(intensity);
}
}
chroma = new Chromatogram(rts.ToArray(), intensities.ToArray());
}
conn.Close();
}
//Input method
public void ReadInMaster()
{
conn = new SQLiteConnection(@"Data Source=" + parentFile);
conn.Open();
var queryText =
"SELECT s.Name, 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();
Dictionary <int, Feature> tmpFeatureDict = new Dictionary <int, Feature>();
while (reader.Read())
{
name = reader["Name"].ToString();
var mz = double.Parse(reader["mz"].ToString());
var apexRT = double.Parse(reader["ApexRT"].ToString());
var apexIntensity = double.Parse(reader["ApexIntensity"].ToString());
var ID_Number = int.Parse(reader["ID_Number"].ToString());
var smoothFeatureString = reader["SmoothFeatureString"].ToString();
List <RTPeak> smoothPeaks = ConvertFeatureStringToPeakList(smoothFeatureString);
var rawFeatureString = reader["RawFeatureString"].ToString();
List <RTPeak> rawPeaks = ConvertFeatureStringToPeakList(rawFeatureString);
var feat = new Feature();
feat.AverageMZ = mz;
feat.ApexTime = apexRT;
feat.ID_Number = ID_Number;
foreach (var peak in rawPeaks)
{
feat.AddPeak(peak);
}
foreach (var peak in smoothPeaks)
{
feat.AddSmoothPeak(peak);
}
feat.AverageMZ = mz;
feat.maxIntensity = apexIntensity;
tmpFeatureDict.Add(ID_Number, feat);
}
queryText =
"SELECT s.GroupID, s.IsValid, s.NumPeaks, s.ApexRT, s.NIST_ID, s.Name, s.ChEBI_ID, s.IncludedFeatures, s.IsInternalStandard, s.QuantIons, s.PeakList FROM featureGroupTable s";
queryCommand = new SQLiteCommand(queryText, conn);
reader = queryCommand.ExecuteReader();
while (reader.Read())
{
var groupID = int.Parse(reader["GroupID"].ToString());
var isValid = bool.Parse(reader["IsValid"].ToString());
//var isValid = false;
//var isValidString = reader["IsValid"].ToString();
//if (isValidString.Equals("1"))
//{
// isValid = true;
//}
var numPeaks = int.Parse(reader["NumPeaks"].ToString());
var apexRT = double.Parse(reader["ApexRT"].ToString());
var chebiID = reader["ChEBI_ID"].ToString();
var NISTID = reader["NIST_ID"].ToString();
var userName = reader["Name"].ToString();
//var isInternalStandard = bool.Parse(reader["IsInternalStandard"].ToString());
var isInternalStandard = false;
var isInternalStandardString = reader["IsInternalStandard"].ToString();
if (isInternalStandardString.Equals("1"))
{
isInternalStandard = true;
}
var includedFeatureString = reader["IncludedFeatures"].ToString();
var quantIonString = reader["QuantIons"].ToString();
List <MZPeak> quantIons = ConvertPeakListString(quantIonString);
var peakListString = reader["PeakList"].ToString();
List <MZPeak> peakList = ConvertPeakListString(peakListString);
var featureGroup = new FeatureGroup();
featureGroup.groupID = groupID;
featureGroup.ApexTime = apexRT;
featureGroup.finalPeaks = peakList;
foreach (var feat in includedFeatureString.Split(';'))
{
if (!string.IsNullOrEmpty(feat))
{
int id = int.Parse(feat);
featureGroup.allFeatures.Add(tmpFeatureDict[id]);
}
}
var eiSpectrum = new EISpectrum();
//if (isInternalStandard==1)
//{
// eiSpectrum.isInternalStandard = true;
//}
//else
//{
// eiSpectrum.isInternalStandard = false;
//}
eiSpectrum.isInternalStandard = isInternalStandard;
eiSpectrum.FinalEIPeaks.AddRange(peakList);
eiSpectrum.FinalNormalizedEIPeaks.AddRange(peakList);
var norm = new Normalization();
norm.CombineLikeMZPeaks(eiSpectrum.FinalNormalizedEIPeaks);
eiSpectrum.FeatureGroup = featureGroup;
eiSpectrum.ApexTimeEI = apexRT;
eiSpectrum.NISTName = NISTID;
eiSpectrum.UserName = userName;
eiSpectrum.chebiID = chebiID;
//if (isValid == 1)
//{
// eiSpectrum.isValid = true;
//}
//else
//{
// eiSpectrum.isValid = false;
//}
eiSpectrum.isValid = isValid;
eiSpectrum.spectrumID = groupID;
eiSpectrum.quantIons = quantIons;
allSpectra.Add(eiSpectrum);
}
queryText = "SELECT s.TICChroma, s.Name FROM rawFileTable s";
queryCommand = new SQLiteCommand(queryText, conn);
reader = queryCommand.ExecuteReader();
List <double> rts = new List <double>();
List <double> intensities = new List <double>();
name = "";
chroma = null;
while (reader.Read())
{
var tic = reader["TICChroma"].ToString();
name = reader["Name"].ToString();
string[] parts = tic.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]);
rts.Add(rt);
intensities.Add(intensity);
}
}
chroma = new Chromatogram(rts.ToArray(), intensities.ToArray());
}
allFeatures = tmpFeatureDict.Values.ToList();
foreach (var spec in allSpectra)
{
foreach (var feat in spec.FeatureGroup.allFeatures)
{
spec.FeatureGroup.includedFeatureIDs.Add(feat.ID_Number);
}
}
}