Esempio n. 1
0
        /*
         * Returns the protein accessions which are uniquely found in this class (and
         * not found in the passed in protein prophet file).
         */
        public List <String> compareProteins(ProteinProphetFile ppf)
        {
            List <String> uniqueProteins = new List <String>();

            foreach (String proteinAccession in proteinsToPeptides.Keys)
            {
                bool notFoundInOtherPPF = ppf.containsProtein(proteinAccession);
                if (notFoundInOtherPPF)
                {
                    uniqueProteins.Add(proteinAccession);
                }
            }
            return(uniqueProteins);
        }
Esempio n. 2
0
        /*
         * Returns the set of peptides (mapping to a protein accession) found in this
         * protein prophet file but not in the other.
         */
        public Dictionary <String, List <String> > comparePeptides(ProteinProphetFile ppf)
        {
            Dictionary <String, List <String> > uniqueProteinToPeptides = new Dictionary <String, List <String> >();

            foreach (String proteinAccession in proteinsToPeptides.Keys)
            {
                List <String> peptides       = proteinsToPeptides[proteinAccession];
                List <String> uniquePeptides = new List <String>();
                foreach (String peptideSequence in peptides)
                {
                    bool notFoundInOtherPPF = ppf.containsPeptide(proteinAccession, peptideSequence);
                    if (notFoundInOtherPPF)
                    {
                        uniquePeptides.Add(peptideSequence);
                    }
                }
                if (uniquePeptides.Count != 0)
                {
                    uniqueProteinToPeptides.Add(proteinAccession, uniquePeptides);
                }
            }
            return(uniqueProteinToPeptides);
        }