//Properly handles removing a protein and updating FDR's, peptide lists, scan lists
public void RemoveProtein(List <MyProtein> proteins)
{
//For each of this protein's peptide lets see if this peptide still maps to some other protein, or else we should remove it.
foreach (MyProtein p in proteins)
{
MyProteins.MyProteinList.Remove(p);
List <string> remainingProteins = MyProteins.MyProteinList.Select(a => a.Locus).ToList();
List <PeptideResult> peptidesToRemove = new List <PeptideResult>();
foreach (PeptideResult pr in p.PeptideResults)
{
if (pr.MyMapableProteins.Intersect(remainingProteins).ToList().Count == 0)
{
peptidesToRemove.Add(pr);
}
}
foreach (PeptideResult pr in peptidesToRemove)
{
PeptideResult pr2 = MyProteins.MyPeptideList.Find(a => a.PeptideSequence.Equals(pr.CleanedPeptideSequence));
bool removed = MyProteins.MyPeptideList.Remove(pr2);
}
}
MyProteins.RebuildScansFromProteins();
MyFDRResult = FDRStatistics.GenerateFDRStatistics(MyProteins, MyParameters);
NotifyPropertyChanged("MyProteinList");
}
public void Save(string fileName)
{
//Refresh statistics in case anything has changed
MyFDRResult = FDRStatistics.GenerateFDRStatistics(MyProteins, MyParameters);
//Serialize it!
System.IO.FileStream flStream = new System.IO.FileStream(fileName, System.IO.FileMode.Create, System.IO.FileAccess.Write);
BinaryFormatter bf = new BinaryFormatter();
bf.AssemblyFormat = System.Runtime.Serialization.Formatters.FormatterAssemblyStyle.Simple;
bf.TypeFormat = System.Runtime.Serialization.Formatters.FormatterTypeStyle.TypesAlways;
bf.Serialize(flStream, this);
flStream.Close();
}
public ResultPackage
(ProteinManager myProteins,
Parameters parameters,
string databaseUsed,
string sqtDirectory,
bool lockMass
)
{
this.lockMass = lockMass;
this.MyProteins = myProteins;
this.MyParameters = parameters;
this.Database = databaseUsed;
this.SQTDirectory = sqtDirectory;
this.MyFDRResult = FDRStatistics.GenerateFDRStatistics(myProteins, MyParameters);
}