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 XQuantClusteringParameters GetFromScreen()
{
XQuantClusteringParameters cp = new XQuantClusteringParameters();
cp.ClusteringPPM = (int)numericUpDownXICPPM.Value;
List <int> acceptableZ = new List <int>();
string[] cols = Regex.Split(textBoxAcceptableZ.Text, ",");
foreach (string col in cols)
{
acceptableZ.Add(int.Parse(col));
}
cp.AcceptableChargeStates = acceptableZ;
return(cp);
}
private void buttonSEProQ2_Click(object sender, EventArgs e)
{
saveFileDialog1.Filter = "XIC Files (xic)|*.xic";
if (saveFileDialog1.ShowDialog() != System.Windows.Forms.DialogResult.Cancel)
{
buttonProcessXIC.Text = "Working";
this.Update();
XQuant.XQuantClusteringParameters cp = parametersXQuant.MyXQuantClusteringParameters;
cp.MinMS1Counts = 1;
cp.RetainOptimal = true;
cp.OnlyUniquePeptides = false;
cp.MaxParsimony = false;
Core35 XICAnalyzer = new Core35(multipleDirectorySelector1.MyDirectoryDescriptionDictionary, cp);
XICAnalyzer.Serialize(saveFileDialog1.FileName);
MessageBox.Show("XIC file saved successfuly", "Information", MessageBoxButtons.OK, MessageBoxIcon.Information);
buttonProcessXIC.Text = "Process XIC";
}
}
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 Core35(List <DirectoryClassDescription> dcds, XQuantClusteringParameters myClusteringParameters)
{
MyClusterParams = myClusteringParameters;
IdentifiedSequencesInFullDirDict = new Dictionary <string, List <string> >();
MyFastaItems = new List <FastaItem>();
SEProFiles = new List <SEProFileInfo>();
//First we will need to load all SEPros and generate a list of peptides with their respectve quantitations
foreach (DirectoryClassDescription cdc in dcds)
{
FileInfo[] files = new DirectoryInfo(cdc.MyDirectoryFullName).GetFiles("*.sepr", SearchOption.AllDirectories);
SEProFiles.Add(new SEProFileInfo(cdc.MyDirectoryFullName, cdc.ClassLabel, cdc.Description, files.Select(a => a.FullName).ToList()));
foreach (FileInfo fi in files)
{
//Make sure we only have 1 sepro file per directory
if (fi.Directory.GetFiles("*.sepr").Count() != 1)
{
throw new Exception("There can be only one SEPro file per directory; error in directory:\n" + fi.DirectoryName);
}
Console.WriteLine("Loading " + fi.FullName);
ResultPackage rp = ResultPackage.Load(fi.FullName);
//Verify if all equivalent ms1 or raw files are in directory
List <string> filesInSEPro = RemoveExtensions((from sqt in rp.MyProteins.AllSQTScans
select sqt.FileName).Distinct().ToList());
List <string> ms1OrRawOrmzMLFiles = fi.Directory.GetFiles("*.ms1").Select(a => a.Name).Concat(fi.Directory.GetFiles("*.RAW").Select(a => a.Name)).Concat(fi.Directory.GetFiles("*.mzML").Select(a => a.Name)).ToList();
ms1OrRawOrmzMLFiles = RemoveExtensions(ms1OrRawOrmzMLFiles);
//Lets store the fasta items
List <MyProtein> proteinsToAnalyze = new List <MyProtein>();
if (myClusteringParameters.MaxParsimony)
{
proteinsToAnalyze = rp.MaxParsimonyList();
}
else
{
proteinsToAnalyze = rp.MyProteins.MyProteinList;
}
IdentifiedSequencesInFullDirDict.Add(fi.Directory.FullName, proteinsToAnalyze.Select(a => a.Locus).ToList());
foreach (MyProtein p in proteinsToAnalyze)
{
if (!MyFastaItems.Exists(a => a.SequenceIdentifier.Equals(p.Locus)))
{
MyFastaItems.Add(new FastaItem(p.Locus, p.Sequence, p.Description));
}
}
//End storing fasta stuff
foreach (string f in filesInSEPro)
{
if (!ms1OrRawOrmzMLFiles.Contains(f))
{
throw new Exception("All .ms1, .mzML, or Thermo .RAW files must be placed in each corresponding SEPro directory. Error in directory:\n" + fi.DirectoryName + "\nfor file:" + f);
}
}
}
}
Process();
PreparePeptideProteinDictionary();
if (myClusteringParameters.RetainOptimal)
{
RetainOptimalSignal();
}
Console.WriteLine("Done");
}
public void UpdatePanel(XQuantClusteringParameters cp)
{
numericUpDownXICPPM.Value = (int)cp.ClusteringPPM;
textBoxAcceptableZ.Text = string.Join(", ", cp.AcceptableChargeStates);
}
