public void PrepDatabase(string rawFilePath, string outputDirectory)
{
var rawFile = new ThermoRawFile(rawFilePath);
rawFile.Open();
var path = outputDirectory + "\\" + rawFile.Name + "_ExtractedFeatures.gcfeat";
var conn = new SQLiteConnection(@"Data Source=" + path);
conn.Open();
SQLiteIOMethods.CreateTablesInDatabase(conn);
SQLiteIOMethods.AddRawFileEntry(rawFile, conn);
SQLiteIOMethods.AddRawFileTICChroma(rawFile, conn);
SQLiteIOMethods.CreateIndices(conn);
conn.Close();
conn.Dispose();
rawFile.ClearCachedScans();
rawFile.Dispose();
OnFinish();
}
private void extractFeatures()
{
if (currIndex < allRawFileNames.Count)
{
var currRawFileString = allRawFileNames[currIndex];
currRawFile = new ThermoRawFile(currRawFileString);
currRawFile.Open();
var path = outputTextBox.Text + "\\" + currRawFile.Name + "_ExtractedFeatures.gcfeat";
conn = new SQLiteConnection(@"Data Source=" + path);
conn.Open();
rawFileListBox.ClearSelected();
rawFileListBox.SelectedIndex = currIndex;
this.Text = currIndex + "\\" + allRawFileNames.Count + " Deconvolved...";
if (!SQLiteIOMethods.IsExtractionDone(conn))
{
currFDM = new FeatureDetectionMethods(currRawFile);
statusLabel.Text = "Adding Features from " + currRawFile.Name + " to Database...";
currFDM.Progress += deconvolution_Progress;
currFDM.Finished += deconvolution_Finished;
currentThread = new Thread(() => currFDM.StepwiseSetupFinalGroups(currRawFile, conn));
currentThread.Start();
}
else
{
conn.Close();
conn.Dispose();
currRawFile.Dispose();
currIndex++;
extractFeatures();
}
}
else
{
currIndex = 0;
//statusBar.Value = 0;
//statusLabel.Text = "Starting Feature Grouping...";
//GroupFeatures();
currRawFile.ClearCachedScans();
currRawFile.Dispose();
if (conn != null)
{
conn.Close();
conn.Dispose();
}
conn = null;
if (currFDM != null)
{
currFDM.Dispose();
currFDM = null;
}
GC.Collect();
rawFileListBox.ClearSelected();
foreach (Control control in this.Controls)
{
control.Enabled = true;
}
statusBar.Value = 100;
statusLabel.Text = "Done!";
this.Text = "Deconvolution Engine";
}
}
public IEnumerable <Feature> ExtractFeatures(IList <int> scans, double ppmTolerance, int minConsecutiveScans = 5)
{
List <Feature> activeFeatures = new List <Feature>();
List <ThermoMzPeak> outPeaks = new List <ThermoMzPeak>();
rawFile.GetLabeledSpectrum(scans[0]).TryGetPeaks(0, 1000, out outPeaks);
double currRT = rawFile.GetRetentionTime(scans[0]);
//MZPeak[] currentPeaks = currentScan.MassSpectrum.GetPeaks(0, 1000).ToArray();
MZPeak[] currentPeaks = outPeaks.ToArray();
activeFeatures.AddRange(currentPeaks.Select(p => new Feature(p, currRT)));
int counter = 0;
int percent = (scans.Count) / 100;
for (int i = 1; i < scans.Count; i++)
{
rawFile.ClearCachedScans();
if (i % percent == 0)
{
counter++;
if (counter < 100)
{
OnProgressUpdate(0.01);
}
}
MSDataScan <ThermoSpectrum> currentScan = rawFile.GetMsScan(scans[i]);
//currentScan = scans[i];
// outPeaks = new List<ThermoMzPeak>();
// double[,] peakArray = currentScan.MassSpectrum.ToArray();
//for (int j = 0; j < peakArray.Length / 2; j++)
//{
// outPeaks.Add(new MZPeak(peakArray[0, j], peakArray[1, j]));
//}
rawFile.GetLabeledSpectrum(currentScan.SpectrumNumber).TryGetPeaks(0, 1000, out outPeaks);
outPeaks = outPeaks.OrderBy(x => x.MZ).ToList();
//currentPeaks = currentScan.MassSpectrum.GetPeaks(0, 1000).ToArray();
currentPeaks = outPeaks.ToArray();
double rt = currentScan.RetentionTime;
// Order features based on their average m/z which may change each round as new peaks are added
activeFeatures = activeFeatures.OrderBy(feat => feat.AverageMZ).ToList();
// Match all the active features to the current spectrum at a given ppm tolerance
MatchPeaks(activeFeatures, currentPeaks, ppmTolerance, rt);
// Find features that are finished and return them if they pass the filters
int f = 0;
while (f < activeFeatures.Count)
{
var feature = activeFeatures[f];
//DJB
//if (feature.LastAddedTime < rt || feature.CurrentState == PeakState.Tailing)
//NWK
if (feature.MaxRT < rt)
{
//DJB
//if (feature.Count >= minConsecutiveScans && (feature.TotalStates & PeakState.Tailing) == PeakState.Tailing)
//NWK
if (feature.Count >= minConsecutiveScans && CheckPeakRise(feature))
{
yield return(feature);
}
activeFeatures.RemoveAt(f);
}
else
{
f++;
}
}
}
//DJB
//foreach (var feature in activeFeatures.Where(f => f.Count > minConsecutiveScans && f.CurrentState != PeakState.Random))
//NWK
foreach (var feature in activeFeatures.Where(f => f.Count > minConsecutiveScans))
{
if (CheckPeakRise(feature))
{
yield return(feature);
}
}
}
