Ejemplo n.º 1
0
        public void TestParsingManyMods(string modDefsFile)
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            var modFile = Utils.GetTestFile(methodName, modDefsFile.Replace("TEST_FOLDER", Utils.DEFAULT_TEST_FILE_FOLDER));

            if (!modFile.Exists)
            {
                Assert.Ignore("Ignoring test TestParsingManyMods since file not found: " + modFile.FullName);
            }

            var aaSet = new AminoAcidSet(modFile.FullName);
            //aaSet.Display();

            //SequenceLocation.ProteinNTerm
            var residue  = AminoAcid.ProteinNTerm.Residue;
            var location = SequenceLocation.ProteinNTerm;
            var aa       = aaSet.GetAminoAcid(residue, location);

            Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
            foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
            {
                var modification = aaSet.GetModificationParams().GetModification(modIndex);
                Console.WriteLine(modification.Mass);
                //Console.Write("\t" + _modificationParams.GetModification(modIndex));
            }
            Console.WriteLine();
            residue  = AminoAcid.ProteinCTerm.Residue;
            location = SequenceLocation.ProteinCTerm;
            aa       = aaSet.GetAminoAcid(residue, location);
            Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
            foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
            {
                var modification = aaSet.GetModificationParams().GetModification(modIndex);
                Console.WriteLine(modification.Mass);
                //Console.Write("\t" + _modificationParams.GetModification(modIndex));
            }

            //foreach (var aa in AminoAcid.StandardAminoAcidArr)
            //{

            /*
             * var keys = _locationSpecificResidueMap[location].Keys.ToArray();
             * Array.Sort(keys);
             * foreach (var residue in keys)
             * {
             *  var aa = GetAminoAcid(residue, location);
             *  Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
             *  foreach (var modIndex in GetModificationIndices(residue, location))
             *  {
             *      Console.Write("\t" + _modificationParams.GetModification(modIndex));
             *  }
             *  Console.WriteLine();
             * }*/
            //}
        }
Ejemplo n.º 2
0
        public void TestParsingManyMods()
        {
            const string modFilePath = @"\\protoapps\UserData\Jungkap\Lewy\db\Mods.txt";
            var          aaSet       = new AminoAcidSet(modFilePath);
            //aaSet.Display();


            //SequenceLocation.ProteinNTerm
            var residue  = AminoAcid.ProteinNTerm.Residue;
            var location = SequenceLocation.ProteinNTerm;
            var aa       = aaSet.GetAminoAcid(residue, location);

            Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
            foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
            {
                var modification = aaSet.GetModificationParams().GetModification(modIndex);
                Console.WriteLine(modification.Mass);
                //Console.Write("\t" + _modificationParams.GetModification(modIndex));
            }
            Console.WriteLine();
            residue  = AminoAcid.ProteinCTerm.Residue;
            location = SequenceLocation.ProteinCTerm;
            aa       = aaSet.GetAminoAcid(residue, location);
            Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
            foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
            {
                var modification = aaSet.GetModificationParams().GetModification(modIndex);
                Console.WriteLine(modification.Mass);
                //Console.Write("\t" + _modificationParams.GetModification(modIndex));
            }


            //foreach (var aa in AminoAcid.StandardAminoAcidArr)

            /*
             * var keys = _locationSpecificResidueMap[location].Keys.ToArray();
             * Array.Sort(keys);
             * foreach (var residue in keys)
             * {
             *  var aa = GetAminoAcid(residue, location);
             *  Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
             *  foreach (var modIndex in GetModificationIndices(residue, location))
             *  {
             *      Console.Write("\t" + _modificationParams.GetModification(modIndex));
             *  }
             *  Console.WriteLine();
             * }
             * }     */
        }
Ejemplo n.º 3
0
        public static AminoAcid[] GetExtendedAminoAcidArray(AminoAcidSet aaSet)
        {
            var ret            = new List <AminoAcid>();
            var modParam       = aaSet.GetModificationParams();
            var aminoAcidArray = AminoAcid.StandardAminoAcidArr;

            foreach (var aa in aminoAcidArray)
            {
                ret.Add(aa);
                foreach (var modIndex in aaSet.GetModificationIndices(aa.Residue, SequenceLocation.Everywhere))
                {
                    var aa2 = new ModifiedAminoAcid(aa, modParam.GetModification(modIndex));
                    ret.Add(aa2);
                }
            }
            return(ret.ToArray());
        }
Ejemplo n.º 4
0
        public static Modification[] GetTerminalModifications(AminoAcidSet aminoAcidSet)
        {
            var terminalModifications = new HashSet <Modification>();
            var terminalLocations     = new[] { SequenceLocation.ProteinNTerm, SequenceLocation.ProteinCTerm };
            var terminalResidues      = new[] { AminoAcid.ProteinNTerm.Residue, AminoAcid.ProteinCTerm.Residue };
            var modParam = aminoAcidSet.GetModificationParams();

            for (var i = 0; i < terminalLocations.Length; i++)
            {
                var location = terminalLocations[i];
                var residue  = terminalResidues[i];
                foreach (var modIndex in aminoAcidSet.GetModificationIndices(residue, location))
                {
                    var modification = modParam.GetModification(modIndex);
                    terminalModifications.Add(modification);
                }
            }
            return(terminalModifications.ToArray());
        }