//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 = "-----";
}
}
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;
}
}
//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 = "-----";
}
}
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;
}
}
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;
}
}
