Exemple #1
0
        //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");
        }
Exemple #2
0
        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();
        }
Exemple #3
0
        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);
        }