/// <summary>
/// If your started an empty cluster you will need to initiate all new clusters
/// </summary>
/// <param name="thisIon"></param>
public void StartCluster(IonLight thisIon)
{
Sequences = new List <SequenceHit>();
ReferenceMass = thisIon.MZ;
MyIons = new List <IonLight>()
{
thisIon
};
}
public IonCluster(IonLight thisIon, double refMass)
{
Sequences = new List <SequenceHit>();
ReferenceMass = refMass;
MyScans = new List <SQTLight>();
MyIons = new List <IonLight>()
{
thisIon
};
}
public IonCluster(IonLight thisIon)
{
Sequences = new List <SequenceHit>();
ReferenceMass = thisIon.MZ;
MyScans = new List <SQTLight>();
MyIons = new List <IonLight>()
{
thisIon
};
}
/// <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);
}
}
}
/// <summary>
///
/// </summary>
/// <param name="referenceMass">The mass used to obtain the XIC</param>
public void Plot()
{
tabControlTheTabs.Items.Clear();
//Generate a list of colors
List <Tuple <string, double[]> > theColors = new List <Tuple <string, double[]> >();
Type brushesType = typeof(System.Windows.Media.Brushes);
// Get all static properties
var properties = brushesType.GetProperties(BindingFlags.Static | BindingFlags.Public);
foreach (var prop in properties)
{
string name = prop.Name;
SolidColorBrush brush = (SolidColorBrush)prop.GetValue(null, null);
Color color = brush.Color;
theColors.Add(new Tuple <string, double[]>(name, new double[] { color.A, color.R, color.G, color.B }));
//Console.WriteLine("Brush named {0} has RGB colors of {1}{2}{2}", name, color.R, color.G, color.B);
}
PlotModel MyModel = new PlotModel();
MyModel.Title = "Reference m/z : " + ReferenceMass;
//Find the division factor
IonLight mostIntenseIon = new IonLight(0, 0, 0, 0);
foreach (Tuple <int, string, List <IonLight>, List <int> > t in MyData)
{
double maxInt = t.Item3.Select(a => a.Intensity).Max();
IonLight i = t.Item3.Find(a => a.Intensity == maxInt);
if (i.Intensity > mostIntenseIon.Intensity)
{
mostIntenseIon = i;
}
}
//Calculate division factor
double f1 = Math.Floor(Math.Log10(mostIntenseIon.Intensity));
double factor = Math.Pow(10, f1);
Console.WriteLine("Factor = " + factor);
var linearAxis1 = new LinearAxis();
linearAxis1.Title = "Intensity x 10E" + f1;
MyModel.Axes.Add(linearAxis1);
var linearAxis2 = new LinearAxis();
linearAxis2.Title = "Retention time";
linearAxis2.Position = AxisPosition.Bottom;
MyModel.Axes.Add(linearAxis2);
List <Tuple <int, string, List <IonLight>, List <int> > > plotData = MyData;
if ((bool)CheckBoxAlign.IsChecked)
{
plotData = AlignChromatograms(MyData);
}
foreach (var t in plotData)
{
LineSeries ls = new LineSeries();
ls.Title = t.Item2;
List <DataPoint> points = t.Item3.Select(a => new DataPoint(a.RetentionTime, a.Intensity / factor)).ToList();
ls.Points.AddRange(points);
ls.Smooth = true;
ls.MarkerSize = 6;
ls.MarkerType = MarkerType.Circle;
ls.ToolTip = t.Item2;
ScatterSeries ss = new ScatterSeries();
foreach (int scanNo in t.Item4)
{
//Find the closest time from the interpolated vector
int minDistance = t.Item3.Min(a => Math.Abs(a.ScanNumber - scanNo));
IonLight closestIon = t.Item3.Find(a => Math.Abs(a.ScanNumber - scanNo) == minDistance);
double x = closestIon.RetentionTime;
double y = closestIon.Intensity / factor;
ss.Points.Add(new ScatterPoint(x, y));
}
MyModel.Series.Add(ls);
MyModel.Series.Add(ss);
DataGrid dg = new DataGrid();
dg.Background = Brushes.AliceBlue;
dg.ItemsSource = t.Item3;
TabItem ti = new TabItem();
ti.Header = t.Item2;
ti.Content = dg;
tabControlTheTabs.Items.Add(ti);
}
MyPlot.Model = MyModel;
}
