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();
}
/// <summary>
/// We recomend runing this after retaining optimal signal. This will revisit other MS1s to try and find a XIC to reuce the undersampling problem
/// </summary>
public void FillInTheGaps(List <string> peptideWithCharges)
{
//We need to know the acceptable comaprisons.
List <int> groups = MyAssociationItems.Select(a => a.Assosication).Distinct().ToList();
foreach (int group in groups)
{
//Get the stuff from this group
List <AssociationItem> items = MyAssociationItems.FindAll(a => a.Assosication == group);
List <string> seproFiles = items.Select(a => a.Directory + "\\" + a.Directory + ".sepr").ToList();
//Now get all peptides from the group
List <QuantPackage2> relevantQuantPackages = (from qpackg in myQuantPkgs
where items.Exists(a => qpackg.FullDirPath.Contains(a.Directory) && a.FileName.Equals(qpackg.FileName))
select qpackg).ToList();
//Load all MS1s to RAM
List <XICGet5> myGetters = new List <XICGet5>(items.Count);
foreach (AssociationItem ai in items)
{
//Find out the full directory
string dtmp = @"\" + ai.Directory;
List <string> seprof = (from s in SEProFiles
from d in s.MyFilesFullPath
where d.Contains(dtmp + "\\")
select d).ToList();
foreach (string s in seprof)
{
FileInfo f = new FileInfo(s);
//We need to find out if we are dealing with .ms2, .RAW or .mzML
string theExtension = GetExtension(f);
string fileName = f.Directory.FullName + @"\" + Regex.Replace(ai.FileName, ".sqt", theExtension);
myGetters.Add(new XICGet5(fileName));
}
}
peptideWithCharges.Sort();
foreach (string peptideWithZ in peptideWithCharges)
{
string[] cols = Regex.Split(peptideWithZ, "::");
string peptide = cols[0];
int z = int.Parse(cols[1]);
//Find out which one has the greatest XIC
List <QuantPackage2> qpSearch = relevantQuantPackages.FindAll(a => a.MyQuants.ContainsKey(peptide));
List <Quant> refQuants = (from qpckg in qpSearch
from quant in qpckg.MyQuants[peptide]
where quant.Z == z && quant.QuantArea > 0
select quant).OrderByDescending(a => a.QuantArea).ToList();
if (refQuants.Count == 0)
{
continue;
}
List <IonLight> MyIonsLight = refQuants[0].GetIonsLight();
List <string> fileNames = (from qpckg in qpSearch
from quant in qpckg.MyQuants[peptide]
where quant.Z == z && quant.QuantArea > 0
select qpckg.FullDirPath + @"\" + qpckg.FileName).Distinct().ToList();
//Find out the tolerance i.e., the XIC above +- the tolerance
double lowerBound = MyIonsLight.Min(a => a.RetentionTime) - (double)ChromeAssociationTolerance;
double upperBound = MyIonsLight.Max(a => a.RetentionTime) + (double)ChromeAssociationTolerance;
//Extract the XICs of this peptide in the not found ones and add them
//Find the missing getters
List <string> fileGetters = myGetters.Select(a => a.MyFile.FullName).ToList();
List <string> fileQuants = new List <string>();
string theExtension = null;
foreach (string fName in fileNames)
{
theExtension = GetExtension(new FileInfo(fName));
fileQuants.Add(Regex.Replace(fName, ".sqt", theExtension));
}
List <string> missing = fileGetters.FindAll(a => !fileQuants.Contains(a)).ToList();
List <XICGet5> gettersToUse = myGetters.FindAll(a => missing.Contains(a.MyFile.FullName));
foreach (XICGet5 xg in gettersToUse)
{
//The problem is it is getting the reference mass of onw charge when it is supposed to be the other
double mz = refQuants[0].PrecursorMZ;
double ppmTol = MyClusterParams.ClusteringPPM;
double minCurrent = MyClusterParams.MinMaxSignal;
double minGapForItemsInCluster = MyClusterParams.MinTimeGapFromItemsInCluster;
//Find out a good scan number
double maxInt = MyIonsLight.Max(a => a.Intensity);
IonLight maxIntIon = MyIonsLight.Find(a => a.Intensity == maxInt);
double Ctolerance = (double)ChromeAssociationTolerance;
double[,] cluster = xg.GetXIC3(mz, ppmTol, maxIntIon.RetentionTime);
if (cluster != null)
{
string tmpf = xg.MyFile.Name;
tmpf = Regex.Replace(tmpf, theExtension, ".sqt");
tmpf = Regex.Replace(tmpf, theExtension, ".sqt");
QuantPackage2 qp = myQuantPkgs.Find(a => a.FullDirPath.Equals(xg.MyFile.Directory.FullName) && a.FileName.Equals(tmpf));
Quant q = new Quants.Quant(cluster, -1, z, mz);
if (qp.MyQuants.ContainsKey(peptide))
{
qp.MyQuants[peptide].Add(q);
}
else
{
qp.MyQuants.Add(peptide, new List <Quant>()
{
q
});
}
}
}
Console.WriteLine(peptide);
}
}
}
