Exemple #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();
             * }*/
            //}
        }
Exemple #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();
             * }
             * }     */
        }
Exemple #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());
        }
Exemple #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());
        }
Exemple #5
0
        /// <summary>
        /// Build the data graph from a sequence graph.
        /// </summary>
        private void BuildGraph()
        {
            var sequenceRev = _sequence.Reverse();
            var sequence    = sequenceRev.Aggregate(string.Empty, (current, aa) => current + aa);

            sequence = "\0" + sequence;
            vertices = new DataVertex[_maxSeqIndex][];
            var mods       = AminoAcidSet.GetModificationParams();
            var id         = 0;
            var ntermIndex = 0;
            var start      = _maxSeqIndex - 2;
            var end        = 0;
            var offset     = 1;

            if (nterminal != null)
            {
                start++;
                sequence += nterminal.Residue;
            }

            if (cterminal != null)
            {
                end--;
                offset   = 0;
                sequence = sequence.Insert(1, cterminal.Residue.ToString(CultureInfo.InvariantCulture));
            }

            // create vertices
            for (var si = start; si > end; si--)
            {
                var graphSi = si - offset;
                vertices[graphSi] = new DataVertex[_graph[si].Length];
                for (var mi = 0; mi < _graph[si].Length; mi++)
                {
                    var node = _graph[si][mi];
                    var mod  = mods.GetModificationCombination(node.ModificationCombinationIndex);
                    SetSink(mi);
                    vertices[graphSi][mi] = new DataVertex
                    {
                        ID                      = id++,
                        NTermIndex              = ntermIndex,
                        ModIndex                = mi,
                        PrefixComposition       = GetComplementaryComposition(si, mi),
                        SuffixComposition       = GetComposition(si, mi),
                        ModificationCombination = mod,
                        Text                    = string.Empty
                    };
                    var vertex = vertices[graphSi][mi];
                    DataGraph.AddVertex(vertex);
                }

                ntermIndex++;
            }

            // connect vertices
            for (var si = start; si > (end + 1); si--)
            {
                var graphSi = si - offset;
                for (var mi = 0; mi < _graph[si].Length; mi++)
                {
                    var node       = _graph[si][mi];
                    var currVertex = vertices[graphSi][mi];
                    foreach (var nextModIndex in node.GetPrevNodeIndices())
                    {
                        var nextVertex     = vertices[graphSi - 1][nextModIndex];
                        var currVertexMods = currVertex.ModificationCombination.Modifications;
                        var nextVertexMods = nextVertex.ModificationCombination.Modifications;
                        var result         = new List <Modification>(currVertexMods);
                        foreach (var mod in nextVertexMods)
                        {
                            if (result.Contains(mod))
                            {
                                result.Remove(mod);
                            }
                        }

                        AminoAcid aminoAcid;
                        if (si == start && nterminal != null)
                        {
                            aminoAcid = nterminal;
                        }
                        else if (si == end + 2 && cterminal != null)
                        {
                            aminoAcid = cterminal;
                        }
                        else
                        {
                            aminoAcid = AminoAcidSet.GetAminoAcid(sequence[graphSi]);
                        }

                        var          modAa        = aminoAcid as ModifiedAminoAcid;
                        Modification aminoAcidMod = null;
                        if (modAa != null)
                        {
                            aminoAcidMod = modAa.Modification;
                        }

                        if (aminoAcidMod != null)
                        {
                            result.Add(aminoAcidMod);
                        }

                        var edgeModifications = new ModificationCombination(result);
                        var edge = new DataEdge(currVertex, nextVertex)
                        {
                            AminoAcid     = aminoAcid,
                            SequenceIndex = graphSi,
                            Modifications = edgeModifications
                        };

                        DataGraph.AddEdge(edge);
                    }
                }
            }
        }