public static void Main(String[] args)
{
String connectionString = @"Persist Security Info=False;User ID=pathcase;Password=dblab;Initial Catalog=polyposisdb_large3;Data Source=127.0.0.1;";
Database db = new Database(connectionString);
//open the database
db.OpenConnection();
if (args[0] == "label")
{
int PedigreeID = Convert.ToInt32(args[1]);
EGDL egdl = new EGDL(db);
DateTime start = DateTime.Now;
egdl.EGDLEncoding(PedigreeID);
TimeSpan time = DateTime.Now.Subtract(start);
Console.WriteLine(time.TotalMilliseconds + " ms");
Console.WriteLine("Finished!");
}
else if (args[0] == "average_inbreeding")
{
int PedigreeID = Convert.ToInt32(args[1]);
InbreedingCalculation ic = new InbreedingCalculation(db, PedigreeID);
double t = ic.AverageIC();
Console.WriteLine("Inbreeding Coefficient: " + t);
}
else if (args[0] == "average_nc")
{
int PedigreeID = Convert.ToInt32(args[1]);
InbreedingCalculation ic = new InbreedingCalculation(db, PedigreeID);
double t = ic.AverageICNC();
Console.WriteLine("Inbreeding Coefficient: " + t);
}
else if (args[0] == "test")
{
int PedigreeID = Convert.ToInt32(args[1]);
InbreedingCalculation ic = new InbreedingCalculation(db, 0);
Console.WriteLine(ic.CalculateNC(",1,1", "#,1#.0.0#,1,0#.0.0.0%.0.0.0%,1,1"));
}
//Console.Read();
//close the database
db.CloseConnection();
}
/// <summary>
/// The constructor
/// </summary>
/// <param name="individualEGDL">The EGDL code of an individual</param>
/// <param name="db">The database connection</param>
public InbreedingCalculation(Database db, int PedigreeID)
{
localGraph = new Graph(db);
currentPedigree = PedigreeID;
egdls = null;
}
/// <summary>
/// The graph is stored in the database, so the
/// input parameter of the constructor is an instance of the database
/// </summary>
/// <param name="conn">A databse instance</param>
public Graph(Database conn)
{
db = conn;
}
/// <summary>
/// The constructor of EGDL class uses a database instance as its input parameter.
/// The reason is that we have to access to the databse frequently, and it's better to open the
/// database once, do all the tasks and then close it.
/// </summary>
/// <param name="conn">The connection string of the database</param>
public EGDL(Database conn)
{
//using the database conn to initilize the local graph object
localGraph = new Graph(conn);
}
