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();
}
