private void buttonXtract_Click(object sender, EventArgs e)
{
if (textBoxScanNo.Text.Length == 0)
{
MessageBox.Show("Please enter a valid scan number");
return;
}
double theoreticalMH = double.Parse(textBoxTheoreticalMass.Text);
int scanNo = int.Parse(textBoxScanNo.Text);
SQTLight s = new SQTLight(null);
s.PeptideSequenceCleaned = "N/A";
XQuantClusteringParameters myParams = parameters1.GetFromScreen();
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
Dictionary <string, List <Quant> > theQuants = Core35.Quant(getter, s, theoreticalMH, isotopicSignal, scanNo, myParams);
stopwatch.Stop();
Console.WriteLine("Time elapsed: {0}", stopwatch.Elapsed);
foreach (var kvp in theQuants)
{
foreach (Quant q in kvp.Value)
{
//XICViewer viewer = new XICViewer();
//viewer.Plot(q.PrecursorMZ, q.GetIonsLight(), new List<int>() { q.ScanNoMS2 });
//viewer.ShowDialog();
}
}
}
public static Core35 DeserializeJSON(string fileName)
{
StreamReader sr = new StreamReader(fileName);
Core35 c = JsonConvert.DeserializeObject <Core35>(
sr.ReadToEnd());
sr.Close();
return(c);
}
public static Core35 Deserialize(string fileName)
{
Stream stream = File.Open(fileName, FileMode.Open);
BinaryFormatter bformatter = new BinaryFormatter();
Core35 core = (Core35)bformatter.Deserialize(stream);
stream.Close();
//Make sure we are loading something clean
core.RemoveDuplicateQuants();
return(core);
}
public void UpdateCoreWithLabels(Core35 theCore)
{
for (int y = 0; y < dataGridViewQuantPckgs.Rows.Count; y++)
{
string dir = dataGridViewQuantPckgs.Rows[y].Cells[0].Value.ToString();
int index = theCore.myQuantPkgs.FindIndex(a => a.FullDirPath.Equals(dir));
if (index == -1)
{
throw new Exception("Error in class assignment linkage.");
}
int lbl = int.Parse(dataGridViewQuantPckgs.Rows[y].Cells[1].Value.ToString());
theCore.myQuantPkgs[index].ClassLabel = lbl;
int index2 = theCore.MyAssociationItems.FindIndex(a => a.FileName.Equals(theCore.myQuantPkgs[index].FileName) && dir.Contains(a.Directory));
theCore.MyAssociationItems[index2].Label = lbl;
}
}
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();
}
