public void DisplayProtein(MyProtein p)
{
myProtein = p;
ListBoxFiles.Items.Clear();
List <String> fileNames = (from pep in p.PeptideResults
from scan in pep.MyScans
select scan.FileName).Distinct().ToList();
fileNames.Sort();
CheckBox chk = new CheckBox();
chk.IsChecked = true;
chk.Content = "AllFiles";
ListBoxFiles.Items.Add(chk);
foreach (string fileName in fileNames)
{
CheckBox chk2 = new CheckBox();
chk2.Content = fileName;
ListBoxFiles.Items.Add(chk2);
}
Plot();
}
public void FireUpInterface(List <MyProtein> theProteinsInGroup, MyProtein p)
{
sequenceViewer1.DisplayProtein(p);
MyProteinGroup = theProteinsInGroup;
ThisProtein = p;
string Locus = p.Locus;
string FastaSequence = p.Sequence;
List <string> Peptides = p.PeptideResults.Select(a => a.PeptideSequence).ToList();
globalProteinCoverage1.Plot(Locus, FastaSequence, Peptides);
}
public ProtQuant(MyProtein theProtein, List <PepQuant> theQuants)
{
int successPos = 0;
int successNeg = 0;
Protein = theProtein;
ThePepQuants = theQuants;
List <double> globalFold = new List <double>();
List <double> correctedTTests = new List <double>();
List <double> uncorrectedTTests = new List <double>();
List <double> w = new List <double>();
foreach (PepQuant pq in theQuants)
{
if (pq.AVGLogFold > 0)
{
successPos++;
}
else
{
successNeg++;
}
globalFold.Add(pq.AVGLogFold);
correctedTTests.Add(pq.CorrectedTTest);
uncorrectedTTests.Add(pq.TTest);
w.Add(1);
}
double bin = 0;
if (successPos > successNeg)
{
bin = alglib.binomialcdistribution(successPos - 1, theQuants.Count, 0.5);
}
else if (successNeg > successPos)
{
bin = alglib.binomialcdistribution(successNeg - 1, theQuants.Count, 0.5);
}
else
{
bin = 0.5;
}
Binomial = bin;
GlobalFold = globalFold.Average();
Stauffers = PatternTools.pTools.StouffersMethod(correctedTTests);
UncorrectedStauffer = PatternTools.pTools.StouffersMethod(uncorrectedTTests);
}
private void dataGridProteins_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
try
{
MyProtein p = (MyProtein)dataGridProteins.SelectedItem;
MyProtein r = ResultViewerResultPackage.MyProteins.MyProteinList.Find(a => a.Locus.Equals(p.Locus));
List <SQTScan> toDisplay = PatternTools.ObjectCopier.Clone(r.Scans);
dataGridPeptides.ItemsSource = toDisplay;
}
catch (Exception e4)
{
Console.WriteLine("Couldn't plot protein : " + e4.Message);
}
}
private void buttonGo_Click(object sender, EventArgs e)
{
saveFileDialog1.Filter = "Fasta Files | *.fasta";
if (saveFileDialog1.ShowDialog() != System.Windows.Forms.DialogResult.Cancel)
{
//Extract IDs
string[] lines = Regex.Split(richTextBoxFastaIDs.Text, "\n");
List <FastaItem> fastaItems = new List <FastaItem>(lines.Length);
foreach (string line in lines)
{
string[] cols = Regex.Split(line, "\t");
int index = MyRP.MyProteins.MyProteinList.FindIndex(a => a.Locus.Equals(cols[0]));
if (index == -1)
{
Console.WriteLine("Locus " + cols[0] + "not found in the results");
continue;
}
MyProtein prot = MyRP.MyProteins.MyProteinList[index];
FastaItem fi = new FastaItem();
fi.Description = prot.Description;
fi.Sequence = prot.Sequence;
fi.SequenceIdentifier = prot.Locus;
fastaItems.Add(fi);
}
//And now save the fasta sequences
StreamWriter sw = new StreamWriter(saveFileDialog1.FileName);
foreach (FastaItem fi in fastaItems)
{
sw.WriteLine(">" + fi.SequenceIdentifier + " " + fi.Description);
sw.WriteLine(fi.Sequence);
}
sw.Close();
MessageBox.Show("Fasta sequences saved");
this.Close();
}
}
public ProtQuant(MyProtein myProtein, double p)
{
Protein = myProtein;
P = p;
//Calculate the fold change
List <double> class1 = new List <double>();
List <double> class2 = new List <double>();
foreach (SQTScan sqt in myProtein.Scans)
{
class1.Add(sqt.Quantitation[0].GetRange(0, 3).Average());
class2.Add(sqt.Quantitation[0].GetRange(3, 3).Average());
}
Fold = class1.Average() / class2.Average();
}
//Show sequence coverage
private void dataGridProteins_MouseDoubleClick(object sender, MouseButtonEventArgs e)
{
try
{
MyProtein p = (MyProtein)dataGridProteins.SelectedItem;
MyProtein r = searchableProteinList.Find(a => a.Locus.Equals(p.Locus));
List <MyProtein> proteinsInGroups = ResultViewerResultPackage.MyProteins.MyProteinList.FindAll(a => a.GroupNo == p.GroupNo);
SequenceExplorer svf = new SequenceExplorer();
svf.FireUpInterface(proteinsInGroups, p);
svf.Show();
}
catch (Exception e7)
{
Console.WriteLine("Unable to plot protein sequence; reason: " + e7.Message);
}
}
public void GenerateGraph(List <MyProtein> myProteins, MyProtein mainProtein)
{
g = new Graph("Protein Group");
foreach (MyProtein p in myProteins)
{
g.AddNode(p.Locus);
}
Node n = g.FindNode(mainProtein.Locus);
n.Attr.Fontcolor = Microsoft.Glee.Drawing.Color.Red;
List <GraphLink> theLinks = new List <GraphLink>();
foreach (MyProtein p in myProteins)
{
List <MyProtein> linkedProteins = myProteins.FindAll(a => a.DistinctPeptides.Intersect(p.DistinctPeptides).ToList().Count > 0);
linkedProteins.Remove(p);
foreach (MyProtein mp in linkedProteins)
{
if (!theLinks.Exists(a => a.To.Equals(p.Locus) && a.From.Equals(mp.Locus)))
{
theLinks.Add(new GraphLink(mp.Locus, p.Locus));
Edge e = new Edge(p.Locus, "", mp.Locus);
e.Attr.ArrowHeadAtTarget = ArrowStyle.None;
if (mp.Locus.Equals(mainProtein.Locus) || p.Locus.Equals(mainProtein.Locus))
{
e.Attr.Color = Microsoft.Glee.Drawing.Color.Red;
}
g.Edges.Add(e);
}
else
{
}
}
}
gViewer.Graph = g;
}
