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;
}
}
public static Mutation getMutationById(string mutId)
{
Mutation toReturn = null;
try
{
List <String> mutationDetails = LocalDbDAL.getMutationByID(mutId);
if (mutationDetails != null)
{
string tempMutId = mutationDetails.ElementAt(0);
string tempChrom = mutationDetails.ElementAt(1);
int tempPosition = Convert.ToInt32(mutationDetails.ElementAt(2));
string tempGeneName = mutationDetails.ElementAt(3);
char tempRefNuc = Convert.ToChar(mutationDetails.ElementAt(4));
char tempVarNuc = Convert.ToChar(mutationDetails.ElementAt(5));
char tempStrand = Convert.ToChar(mutationDetails.ElementAt(6));
string tempChromNum = mutationDetails.ElementAt(7);
string tempRefCodon = mutationDetails.ElementAt(8);
string tempVarCodon = mutationDetails.ElementAt(9);
string tempRefAA = mutationDetails.ElementAt(10);
string tempVarAA = mutationDetails.ElementAt(11);
string tempPMutationName = mutationDetails.ElementAt(12);
string tempCMutationName = mutationDetails.ElementAt(13);
string tempCosmicName = mutationDetails.ElementAt(14);
toReturn = new Mutation(tempMutId, tempChrom, tempPosition, tempGeneName, tempRefNuc, tempVarNuc, tempStrand, tempChromNum, tempRefCodon, tempVarCodon, tempRefAA, tempVarAA, tempPMutationName, tempCMutationName, tempCosmicName);
}
}
catch (Exception)
{
throw;
}
return(toReturn);
}
public static List <Patient> getPatientListWithMutation(string mutationId)
{
List <Patient> toReturn = null;
try
{
List <List <string> > patient = LocalDbDAL.getPatientListByMutation(mutationId);
if (patient != null)
{
toReturn = new List <Patient>();
foreach (List <string> l in patient)
{
string testName = l.ElementAt(0);
string patientId = l.ElementAt(1);
string fName = l.ElementAt(2);
string lName = l.ElementAt(3);
string pathoNum = l.ElementAt(4);
string runNum = l.ElementAt(5);
string tumourSite = l.ElementAt(6);
string diseaseLevel = l.ElementAt(7);
string background = l.ElementAt(8);
string prevTreatment = l.ElementAt(9);
string currTreatment = l.ElementAt(10);
string conclusion = l.ElementAt(11);
Patient p = new Patient(testName, patientId, fName, lName, pathoNum, runNum, tumourSite, diseaseLevel, background, prevTreatment, currTreatment, conclusion);
toReturn.Add(p);
}
}
}
catch (Exception)
{
throw;
}
return(toReturn);
}
public static void addMatch(string testName, string mutId)
{
try
{
LocalDbDAL.addMatch(testName, mutId);
}
catch (Exception)
{
throw;
}
}
public static void updatePatient(string testName, string id, string fName, string lName, string pathologicalNum, string runNum, string tumourSite, string deseaseLevel, string prevTreatment, string currTreatment, string background, string conclusion)
{
try
{
LocalDbDAL.updatePatient(testName, id, fName, lName, pathologicalNum, runNum, tumourSite, deseaseLevel, prevTreatment, currTreatment, background, conclusion);
}
catch (Exception)
{
throw;
}
}
public static int getNumOfPatientWithSameMutation(string mutationId)
{
try
{
return(LocalDbDAL.getNumOfPatientWithSameMutation(mutationId));
}
catch (Exception)
{
throw;
}
}
public static bool patientExistByTestName(string testName)
{
try
{
return(LocalDbDAL.patientExist(testName));
}
catch (Exception)
{
throw;
}
}
public static bool mutationExist(Mutation mutation)
{
try
{
return(LocalDbDAL.mutationExist(mutation.Chrom, mutation.Position, mutation.Ref, mutation.Var));
}
catch (Exception)
{
throw;
}
}
public static void addMutation(Mutation m)
{
try
{
LocalDbDAL.addMutation(m.MutId, m.Chrom, m.Position, m.GeneName, m.Ref, m.Var, m.Strand, m.ChromNum, m.RefCodon, m.VarCodon, m.RefAA, m.VarAA, m.PMutationName, m.CMutationName, m.CosmicName);
}
catch (Exception)
{
throw;
}
}
public static List <Mutation> getMutationListByTestName(string testName)
{
List <Mutation> toReturn = null;
try
{
List <string> tempList = LocalDbDAL.getMutationListPerPatient(testName);
toReturn = new List <Mutation>();
foreach (string s in tempList)
{
toReturn.Add(getMutationById(s));
}
}
catch (Exception)
{
throw;
}
return(toReturn);
}
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;
}
}