public static void AddFeatureGroupToDatabase(FeatureGroup group, int ID_Num, SQLiteConnection conn)
{
//(GroupID INT, NumPeaks INT, ApexRT DOUBLE, IncludedFeatures TEXT)
var insertText = "INSERT INTO featureGroupTable (GroupID, NumPeaks, ApexRT, IncludedFeatures, PeakList)"
+ " VALUES (@GroupID, @NumPeaks, @ApexRT, @IncludedFeatures, @PeakList)";
var insertCommand = new SQLiteCommand(insertText, conn);
insertCommand.Parameters.AddWithValue("@GroupID", ID_Num);
insertCommand.Parameters.AddWithValue("@NumPeaks", group.allFeatures.Count);
insertCommand.Parameters.AddWithValue("@ApexRT", group.ApexTime);
var includedFeatures = "";
foreach (var feat in group.allFeatures)
{
includedFeatures += feat.ID_Number + ";";
}
insertCommand.Parameters.AddWithValue("@IncludedFeatures", includedFeatures);
var peakList = "";
foreach (var peak in group.finalPeaks)
{
peakList += peak.MZ + "," + peak.Intensity + ";";
}
insertCommand.Parameters.AddWithValue("@PeakList", peakList);
insertCommand.ExecuteNonQuery();
}
public void GetMainSubgroup(FeatureGroup group)
{
FeatureGroup mainSubGroup = new FeatureGroup();
double startTime = group.ApexTime - .005;
double stopTime = group.ApexTime + .005;
startTime = group.ApexTime;
stopTime = group.ApexTime;
Tuple <double, double> apexWindow = GetApexTimeWindow(group.allFeatures.First(), GetRTPeakIndex(group.allFeatures.First(), group.allFeatures.First().MaxPeak));
startTime = apexWindow.Item1;
stopTime = apexWindow.Item2;
foreach (Feature feature in group.allFeatures)
{
if (ApexCheck(feature, startTime, stopTime))
{
mainSubGroup.AddFeature(feature);
}
}
mainSubGroup.ApexTime = group.ApexTime;
mainSubGroup.DoApexCalculations();
group.mainSubGroup = mainSubGroup;
group.SubGroups.Add(mainSubGroup);
}
private IEnumerable <FeatureGroup> GroupFeatures(IEnumerable <Feature> features, double time, int minNumberFragments = 5)
{
List <Feature> totalFeatures = features.OrderByDescending(f => f.MaxIntensity).ToList();
while (totalFeatures.Count > 0)
{
Feature maxfeature = totalFeatures[0];
totalFeatures.RemoveAt(0);
double maxFeatureApex = maxfeature.ApexTime;
FeatureGroup group = new FeatureGroup(maxfeature);
group.ApexTime = maxFeatureApex;
double minTime = maxFeatureApex - time / 2;
double maxTime = maxFeatureApex + time / 2;
int i = 0;
while (i < totalFeatures.Count)
{
var feature = totalFeatures[i];
if (minTime <= feature.ApexTime && feature.ApexTime <= maxTime)
{
group.AddFeature(feature);
totalFeatures.RemoveAt(i);
}
else
{
i++;
}
}
if (group.Count >= minNumberFragments)
{
yield return(group);
}
}
}
public void GetFeatureSubGroups(FeatureGroup group)
{
group.allFeatures = group.allFeatures.OrderByDescending(x => x.MaxPeak.Intensity).ToList();
foreach (Feature feature in group.allFeatures)
{
feature.includedInSubGroup = false;
}
group.maxFeature = group.allFeatures[0];
GetFeatureSubGroups(group, 0, 0);
}
public List <MZPeak> GetPeaksFromNearestSpectrum(FeatureGroup group, ThermoRawFile rawFile)
{
int scanNum = rawFile.GetSpectrumNumber(group.ApexTime);
List <MZPeak> returnPeaks = new List <MZPeak>();
ThermoSpectrum spectrum = rawFile.GetLabeledSpectrum(scanNum);
HashSet <double> peakMZs = new HashSet <double>();
foreach (Feature feature in group.allFeatures)
{
MZPeak outPeak = spectrum.GetClosestPeak(MassRange.FromPPM(feature.AverageMZ, 10));
if (outPeak != null)
{
if (!peakMZs.Contains(outPeak.Intensity))
{
returnPeaks.Add(new MZPeak(feature.AverageMZ, outPeak.Intensity));
peakMZs.Add(outPeak.Intensity);
}
}
}
returnPeaks = returnPeaks.OrderBy(x => x.MZ).ToList();
return(returnPeaks);
}
public void GetFeatureSubGroups(FeatureGroup group, int nextSubGroupPointer, int numFeaturesInSubGroups)
{
bool nextSubGroupPointerFound = false;
if (numFeaturesInSubGroups != group.allFeatures.Count)
{
Feature maxFeature = group.allFeatures[nextSubGroupPointer];
// if (maxFeature.MaxPeak.Intensity < group.maxFeature.MaxPeak.Intensity * .06 || maxFeature.MaxPeak.Intensity < 100000 )
if (maxFeature.MaxPeak.Intensity < group.maxFeature.MaxPeak.Intensity * .06)
{
return;
}
//Binary search to the appropriate index (you'll need to store the actual RTPeak instead of just the intensity and time)
int startIndex = GetRTPeakIndex(maxFeature, maxFeature.MaxPeak);
//Get the apex time window for 93.5% intensity threshold
Tuple <double, double> ApexTimeWindow = GetApexTimeWindow(maxFeature, startIndex);
//Create a new subgroup, add the feature to the subgroup.
FeatureGroup newSubGroup = new FeatureGroup(maxFeature);
newSubGroup.ApexTime = maxFeature.ApexTime;
//Check whether this has been included in a sub group. If not set that flag to true and increment numFeaturesInSubGroups.
if (!maxFeature.includedInSubGroup)
{
maxFeature.includedInSubGroup = true;
numFeaturesInSubGroups++;
}
maxFeature.numSubGroups++;
//Iterate over all features in the group and see if their apexes align
for (int i = 0; i < group.allFeatures.Count; i++)
{
//Check whether there is an apex for the feature if (ApexCheck(feature, 93.5 start, 93.5 stop))... Add to subgroup, if Feature hasn't been in a subgroup yet
if (i != nextSubGroupPointer)
{
Feature currFeature = group.allFeatures[i];
if (ApexCheck(currFeature, ApexTimeWindow.Item1, ApexTimeWindow.Item2))
{
newSubGroup.AddFeature(currFeature);
if (!currFeature.includedInSubGroup)
{
currFeature.includedInSubGroup = true;
numFeaturesInSubGroups++;
}
currFeature.numSubGroups++;
}
else
{
if (i > nextSubGroupPointer && !nextSubGroupPointerFound && !currFeature.includedInSubGroup)
{
nextSubGroupPointer = i;
nextSubGroupPointerFound = true;
}
}
}
}
newSubGroup.DoApexCalculations();
if (newSubGroup.allFeatures.Count > 1)
{
group.SubGroups.Add(newSubGroup);
}
GetFeatureSubGroups(group, nextSubGroupPointer, numFeaturesInSubGroups);
}
}
