private void buttonLoad_Click(object sender, EventArgs e)
{
if (openFileDialog1.ShowDialog() != DialogResult.Cancel)
{
Console.WriteLine("Loading file " + openFileDialog1.FileName);
getter = new XICGet5(openFileDialog1.FileName);
buttonLoad.Text = openFileDialog1.FileName;
groupBoxXtract.Enabled = true;
}
}
public static Dictionary <string, List <Quant> > Quant(XICGet5 xic, SQTLight theScn, double theoreticalMH, SignalGenerator isotopicSignal, int scnNo, XQuantClusteringParameters myParams)
{
Dictionary <string, List <Quant> > theResults = new Dictionary <string, List <Quants.Quant> >();
//We will obtain the isotopic signal and obtain the XIC according to the most intense isotope
List <double> isoSignal = isotopicSignal.GetSignal(5, theoreticalMH, 0);
int maximumSignalIsotope = isoSignal.IndexOf(isoSignal.Max());
foreach (int z in myParams.AcceptableChargeStates)
{
double pMass = ((double)z - 1.0) * 1.007276466;
double iMass = (maximumSignalIsotope * 1.00335);
double mz = (theoreticalMH + pMass + iMass) / (double)z;
double[,] ic = xic.GetXIC3(Math.Round(mz, 4), myParams.ClusteringPPM, scnNo);
if (ic != null)
{
Quant q = new Quants.Quant(ic, theScn.ScanNumber, z, Math.Round(mz, 4));
if (theResults.ContainsKey(theScn.PeptideSequenceCleaned))
{
theResults[theScn.PeptideSequenceCleaned].Add(q);
}
else
{
theResults.Add(theScn.PeptideSequenceCleaned, new List <Quants.Quant>()
{
q
});
}
}
}
return(theResults);
}
public void Process()
{
myQuantPkgs = new List <QuantPackage2>();
SignalGenerator isotopicSignal = new SignalGenerator();
foreach (SEProFileInfo sfi in SEProFiles)
{
foreach (string file in sfi.MyFilesFullPath)
{
Console.WriteLine("Processing for " + file);
ResultPackage rp = ResultPackage.Load(file);
List <string> filesInSEPro = (from sqt in rp.MyProteins.AllSQTScans
select sqt.FileName).Distinct().ToList();
FileInfo fi = new FileInfo(file);
foreach (string msFile in filesInSEPro)
{
QuantPackage2 qp = new QuantPackage2(msFile, fi.Directory.FullName, sfi.ClassLabel);
Console.WriteLine("\t" + msFile);
List <string> ms1OrRawOrmzMLFiles = fi.Directory.GetFiles("*.ms1").ToList().Concat(fi.Directory.GetFiles("*.RAW")).Concat(fi.Directory.GetFiles("*.mzML")).ToList().Select(a => a.Name).ToList();
int fileToRead = ms1OrRawOrmzMLFiles.FindIndex(a => RemoveExtension(a).Equals(RemoveExtension(msFile)));
XICGet5 xic = new XICGet5(fi.DirectoryName + "/" + ms1OrRawOrmzMLFiles[fileToRead]);
List <SQTScan> scansTMP = rp.MyProteins.AllSQTScans.FindAll(a => a.FileName.Equals(msFile));
if (MyClusterParams.OnlyUniquePeptides)
{
int removedForNotUnique = scansTMP.RemoveAll(a => a.IsUnique);
Console.WriteLine("Scans removed for not dealing with unique peptides: " + removedForNotUnique);
}
List <SQTLight> scans = scansTMP.Select(a => new SQTLight(a)).ToList();
int counter = 0;
for (int i = 0; i < scans.Count; i++)
{
Dictionary <string, List <Quant> > theseQuants = Core35.Quant(xic, scans[i], scans[i].TheoreticalMH, isotopicSignal, scans[i].ScanNumber, MyClusterParams);
foreach (var kvp in theseQuants)
{
kvp.Value.RemoveAll(a => a.MyIons.GetLength(1) < MyClusterParams.MinMS1Counts);
if (kvp.Value.Count > 0)
{
if (qp.MyQuants.ContainsKey(kvp.Key))
{
qp.MyQuants[kvp.Key].AddRange(kvp.Value);
}
else
{
qp.MyQuants.Add(kvp.Key, kvp.Value);
}
}
}
counter++;
Console.Write("\rScans Processed: " + counter + "/" + scans.Count);
}
//Store them
myQuantPkgs.Add(qp);
Console.WriteLine("\nTotal quants stored so far = " + myQuantPkgs.Sum(a => a.MyQuants.Count));
Console.WriteLine("Total files analyzed so far = " + myQuantPkgs.Count);
Console.WriteLine("Done procesing :" + msFile);
System.GC.Collect();
System.GC.WaitForPendingFinalizers();
System.GC.Collect();
}
}
}
GenerateAssociationItems();
}