Пример #1
0
        //Method that use the basic details of the mutation and generate all extra details.
        public void extractExtraData()
        {
            try
            {
                //get gene details from lodal db, if not exit create new gene and add it to locel db
                _gene = MainBL.getGene(_geneName, _chrom);
                if (_gene == null)
                {
                    _gene = MainBL.addGene(_geneName, _chrom);
                }

                _strand = _gene.Strand;
                if (_strand.Equals('+'))
                {
                    _cosmicDetails = MainBL.getCosmicDetails(_chromNum, _position, _ref, _var);
                }
                else if (_strand.Equals('-'))
                {
                    _cosmicDetails = MainBL.getCosmicDetails(_chromNum, _position, OppositeNuc(_ref), OppositeNuc(_var));
                }

                setVarRefCodons(_gene.getOffsetInCodon(_position));
            }
            catch (Exception)
            {
                throw;
            }
            //sets the rest of the mutation details.
            if (!_refCodon.Equals("No Coding"))
            {
                _varAA = GeneralMethods.getAminoAcid(_varCodon);
                _refAA = GeneralMethods.getAminoAcid(_refCodon);
            }
            else
            {
                _varAA = "-----";
                _refAA = "-----";
            }
            if (_cosmicDetails != null)
            {
                _cosmicName    = _cosmicDetails.ElementAt(0);
                _pMutationName = _cosmicDetails.ElementAt(1);
                _cMutationName = _cosmicDetails.ElementAt(2);
            }
            else
            {
                _cosmicName    = "-----";
                _pMutationName = "-----";
                _cMutationName = "-----";
            }
        }
Пример #2
0
        public static Gene getGene(string geneName, string chrom)
        {
            Gene          g           = null;
            List <String> geneStrings = null;

            try
            {
                geneStrings = LocalDbDAL.getGene(geneName, chrom);
                if (geneStrings != null)
                {
                    char  strand     = Convert.ToChar(geneStrings[2]);
                    int[] exonStarts = exonStringToIntArray(geneStrings[3]);
                    int[] exonEnds   = exonStringToIntArray(geneStrings[4]);
                    g = new Gene(geneName, chrom, strand, exonStarts, exonEnds);
                }
                return(g);
            }
            catch (Exception)
            {
                throw;
            }
        }
Пример #3
0
        //Method that use the basic details of the mutation and generate all extra details.
        public void extractExtraData()
        {
            try
            {
                //get gene details from lodal db, if not exit create new gene and add it to locel db
                _gene = MainBL.getGene(_geneName, _chrom);
                if (_gene == null)
                    _gene = MainBL.addGene(_geneName, _chrom);

                _strand = _gene.Strand;
                if (_strand.Equals('+'))
                    _cosmicDetails = MainBL.getCosmicDetails(_chromNum, _position, _ref, _var);
                else if (_strand.Equals('-'))
                    _cosmicDetails = MainBL.getCosmicDetails(_chromNum, _position, OppositeNuc(_ref), OppositeNuc(_var));

                setVarRefCodons(_gene.getOffsetInCodon(_position));
            }
            catch (Exception)
            {
                throw;
            }
            //sets the rest of the mutation details.
            if (!_refCodon.Equals("No Coding"))
            {
                _varAA = GeneralMethods.getAminoAcid(_varCodon);
                _refAA = GeneralMethods.getAminoAcid(_refCodon);
            }
            else
            {
                _varAA = "-----";
                _refAA = "-----";
            }
            if (_cosmicDetails != null)
            {
                _cosmicName = _cosmicDetails.ElementAt(0);
                _pMutationName = _cosmicDetails.ElementAt(1);
                _cMutationName = _cosmicDetails.ElementAt(2);
            }
            else
            {
                _cosmicName = "-----";
                _pMutationName = "-----";
                _cMutationName = "-----";
            }
        }
Пример #4
0
        public static Gene getGene(string geneName, string chrom)
        {
            Gene g = null;
            List<String> geneStrings = null;
            try
            {
                geneStrings = LocalDbDAL.getGene(geneName, chrom);
                if (geneStrings != null)
                {
                    char strand = Convert.ToChar(geneStrings[2]);
                    int[] exonStarts = exonStringToIntArray(geneStrings[3]);
                    int[] exonEnds = exonStringToIntArray(geneStrings[4]);
                    g = new Gene(geneName, chrom, strand, exonStarts, exonEnds);
                }
                return g;
            }
            catch (Exception)
            {
                throw;
            }

        }
Пример #5
0
        public static Gene addGene(string geneName, string chrom)
        {
            List<String> geneStrings = null;
            Gene toReturn = null;
            try
            {
                geneStrings = UcscDAL.getGene(geneName, chrom);
                if (geneStrings != null)
                {
                    char strand = Convert.ToChar(geneStrings[0]);
                    int cdsStart = int.Parse(geneStrings[1]);
                    int cdsEnd = int.Parse(geneStrings[2]);
                    int[] exonStars = exonStringToIntArray(geneStrings[4]);
                    int[] exonEnds = exonStringToIntArray(geneStrings[5]);
                    toReturn = new Gene(geneName, chrom, strand, cdsStart, cdsEnd, exonStars, exonEnds);
                    string tempExonStarts = exonIntArrayToString(toReturn.ExonStarts);
                    string tempExonEnds = exonIntArrayToString(toReturn.ExonEnds);

                    LocalDbDAL.addGene(geneName, chrom, strand, tempExonStarts, tempExonEnds);
                }
                return toReturn;
            }
            catch (Exception)
            {
                throw;
            }
        }