コード例 #1
0
ファイル: TestAminoAcidSet.cs プロジェクト: javamng/GitHUB
        public void TestParsingGlycoMods()
        {
            const string modFilePath = @"C:\cygwin\home\kims336\Data\Debug\MSPathFinder_Mods.txt";
            var          aaSet       = new AminoAcidSet(modFilePath);

            aaSet.Display();
        }
コード例 #2
0
        public void TestCreatingAminoAcidSet()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            TestUtils.ShowStarting(methodName);

            // Configure amino acid set
            var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.PeptideNTerm, false);
            var acetylN  = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
            var oxM      = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);

            var searchModifications = new List <SearchModification>
            {
                acetylN,
                pyroGluQ,
                oxM
            };

            const int numMaxModsPerProtein = 2;

            var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);

            //var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
            aaSet.Display();
        }
コード例 #3
0
        public void TestReadingModFile()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            Utils.ShowStarting(methodName);

            var modFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\Mods.txt");
            var modFile     = Utils.GetTestFile(methodName, modFilePath);

            var modFileParser = new ModFileParser(modFile.FullName);

            Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
            foreach (var searhMod in modFileParser.SearchModifications)
            {
                Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
            }
            var aaSet = new AminoAcidSet(modFile.FullName);

            aaSet.Display();
        }
コード例 #4
0
        public void TestReadingModFile()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            TestUtils.ShowStarting(methodName);

            const string modFilePath = @"..\..\..\TestFiles\Mods.txt";

            if (!File.Exists(modFilePath))
            {
                Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modFilePath);
            }

            var modFileParser = new ModFileParser(modFilePath);

            Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
            foreach (var searhMod in modFileParser.SearchModifications)
            {
                Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
            }
            var aaSet = new AminoAcidSet(modFilePath);

            aaSet.Display();
        }