public static void AddQuantPointToDatabase(EISpectrum masterSpecies, double quantIonMZ, double apexIntensity, double offset, Feature quantFeature, string rawName, SQLiteConnection conn)
{
if (!ContainsQuantFeature(masterSpecies.ApexTimeEI, rawName, conn))
{
int id = GetRawFileID(rawName, conn);
//(ID INT, Name TEXT, FeatureRT DOUBLE, QuantIonMZ DOUBLE, ApexIntensity DOUBLE, OffsetRT DOUBLE, FeatureString TEXT)
var insertText = "INSERT INTO rawFileQuantTable (ID, Name, FeatureRT, QuantIonMZ, ApexIntensity, OffsetRT, FeatureString)" +
" VALUES (@ID, @Name, @FeatureRT, @QuantIonMZ, @ApexIntensity, @OffsetRT, @FeatureString)";
var insertCommand = new SQLiteCommand(insertText, conn);
insertCommand.Parameters.AddWithValue("@ID", id);
insertCommand.Parameters.AddWithValue("@Name", rawName);
insertCommand.Parameters.AddWithValue("@QuantIonMZ", quantIonMZ);
insertCommand.Parameters.AddWithValue("@ApexIntensity", apexIntensity);
insertCommand.Parameters.AddWithValue("@OffsetRT", offset);
insertCommand.Parameters.AddWithValue("@FeatureRT", masterSpecies.ApexTimeEI);
var featString = "";
if (quantFeature != null)
{
foreach (var peak in quantFeature.smoothRTPeaks)
{
featString += peak.RT + "," + peak.Intensity + ";";
}
}
insertCommand.Parameters.AddWithValue("@FeatureString", featString);
insertCommand.ExecuteNonQuery();
}
}
public double GetDemoninatorTerm(EISpectrum eiSpec)
{
double returnVal = 0;
foreach (MZPeak peak in eiSpec.FinalNormalizedEIPeaks)
{
returnVal += (peak.MZ * peak.Intensity);
}
return(returnVal);
}
public void StepwiseSetupFinalGroups(ThermoRawFile rawfile, SQLiteConnection conn)
{
List <int> list = new List <int>();
foreach (var scan in rawFile.GetMsScans())
{
if (scan.MsnOrder == 1)
{
list.Add(scan.SpectrumNumber);
}
}
var extractedFeatures = ExtractFeatures(list, 10).ToList();
//Features have been extracted
//Check which features are valid and which are not based on how their max intensity changes
//nwk temp code
var tmpFeatures = extractedFeatures.Where(x => x.ApexTime > 13.55 && x.apexTime <13.70 && x.AverageMZ> 267.082 && x.averageMZ < 267.095).ToList();
var q = "";
CheckPeakRise(extractedFeatures);
//Smooth features now
foreach (Feature feature in extractedFeatures)
{
feature.SmoothRTPeaks = GetRollingAveragePeaks(feature.RawRTPeaks, 9);
}
CheckPeakRiseSmooth(extractedFeatures);
List <Feature> finalFeatures = GetFinalFeatures(extractedFeatures);
extractedFeatures.Clear();
CheckPeakRiseSmooth(finalFeatures);
int count = 1;
foreach (var feat in finalFeatures)
{
feat.ID_Number = count;
count++;
}
//push features to database
PushFeaturesToDatabase(rawfile, finalFeatures, conn);
List <FeatureGroup> groups = GroupFeatures(finalFeatures, .04, 2).ToList();
DoubleBack(groups, finalFeatures);
finalFeatures.Clear();
List <FeatureGroup> allSubGroups = new List <FeatureGroup>();
foreach (FeatureGroup group in groups)
{
GetMainSubgroup(group);
GetFeatureSubGroups(group);
if (group.mainSubGroup.allFeatures.Count > 1)
{
allSubGroups.Add(group.mainSubGroup);
}
foreach (FeatureGroup subGroup in group.SubGroups)
{
allSubGroups.Add(subGroup);
}
}
this.finalGroups = GetFinalFeatures(allSubGroups);
foreach (FeatureGroup group in this.finalGroups)
{
group.finalPeaks = GetPeaksFromNearestSpectrum(group, rawFile);
}
foreach (FeatureGroup group in this.finalGroups)
{
EISpectrum spec = new EISpectrum();
spec.ApexTimeEI = group.ApexTime;
spec.FeatureGroup = group;
spec.FinalEIPeaks = group.finalPeaks;
spec.FinalEIPeaks = spec.FinalEIPeaks.OrderByDescending(x => x.Intensity).ToList();
if (group.finalPeaks.Count >= 2) //here as well (changed to remove num feature restriction)
{
spec.BasePeak = spec.FinalEIPeaks[0];
this.eiSpectra.Add(spec);
}
spec.FinalNormalizedEIPeaks.AddRange(spec.FinalEIPeaks);
spec.FinalNormalizedEIPeaks = spec.FinalNormalizedEIPeaks.OrderBy(x => x.MZ).ToList();
norm.CombineLikeMZPeaks(spec.FinalNormalizedEIPeaks);
spec.AdjustedPeaks.AddRange(spec.FinalNormalizedEIPeaks);
norm.GetAdjustedPeaks(spec.AdjustedPeaks);
spec.DenominatorTerm = norm.GetDemoninatorTerm(spec.AdjustedPeaks);
}
//this.eiSpectra = CleanUpSpectra(eiSpectra);
this.eiSpectra = eiSpectra.Where(x => x.FinalEIPeaks.Count >= 2).ToList();
AddFeatureGroupsToDatabase(this.eiSpectra, conn);
SQLiteIOMethods.ExtractionComplete(conn);
SQLiteIOMethods.GroupingComplete(conn);
OnFinish();
}
private void StepwiseSetupFinalGroups(ThermoRawFile rawFile)
{
List <int> list = new List <int>();
foreach (var scan in rawFile.GetMsScans())
{
if (scan.RetentionTime < 7)
{
list.Add(scan.SpectrumNumber);
}
}
var extractedFeatures = ExtractFeatures(list, 10).ToList();
//Features have been extracted
//Check which features are valid and which are not based on how their max intensity changes
CheckPeakRise(extractedFeatures);
//Smooth features now
foreach (Feature feature in extractedFeatures)
{
feature.SmoothRTPeaks = GetRollingAveragePeaks(feature.RawRTPeaks, 9);
}
CheckPeakRiseSmooth(extractedFeatures);
List <Feature> finalFeatures = GetFinalFeatures(extractedFeatures);
extractedFeatures.Clear();
CheckPeakRiseSmooth(finalFeatures);
List <FeatureGroup> groups = GroupFeatures(finalFeatures, .04, 2).ToList();
DoubleBack(groups, finalFeatures);
finalFeatures.Clear();
List <FeatureGroup> allSubGroups = new List <FeatureGroup>();
foreach (FeatureGroup group in groups)
{
GetMainSubgroup(group);
GetFeatureSubGroups(group);
if (group.mainSubGroup.allFeatures.Count > 1)
{
allSubGroups.Add(group.mainSubGroup);
}
foreach (FeatureGroup subGroup in group.SubGroups)
{
allSubGroups.Add(subGroup);
}
}
this.finalGroups = GetFinalFeatures(allSubGroups);
foreach (FeatureGroup group in this.finalGroups)
{
group.finalPeaks = GetPeaksFromNearestSpectrum(group, rawFile);
}
foreach (FeatureGroup group in this.finalGroups)
{
EISpectrum spec = new EISpectrum();
spec.ApexTimeEI = group.ApexTime;
spec.FeatureGroup = group;
spec.FinalEIPeaks = group.finalPeaks;
spec.FinalEIPeaks = spec.FinalEIPeaks.OrderByDescending(x => x.Intensity).ToList();
if (group.finalPeaks.Count > 6) //here as well (changed to remove num feature restriction)
{
spec.BasePeak = spec.FinalEIPeaks[0];
this.eiSpectra.Add(spec);
}
spec.FinalNormalizedEIPeaks.AddRange(spec.FinalEIPeaks);
spec.FinalNormalizedEIPeaks = spec.FinalNormalizedEIPeaks.OrderBy(x => x.MZ).ToList();
norm.CombineLikeMZPeaks(spec.FinalNormalizedEIPeaks);
spec.AdjustedPeaks.AddRange(spec.FinalNormalizedEIPeaks);
norm.GetAdjustedPeaks(spec.AdjustedPeaks);
spec.DenominatorTerm = norm.GetDemoninatorTerm(spec.AdjustedPeaks);
}
OnFinish();
}
