private static void initiate_Updater()
{
int i = 1;
Console.WriteLine("Connecting to database prokaryote_schema...");
try
{
conn = new MySqlConnection("Server=127.0.0.1;Database=prokaryote_schema;Uid=root;Pwd=Anitar@n@");
conn.Open();
Console.WriteLine("Connected to database prokaryote_schema\n");
newbacteriaspath = new List <string>();
extract_newbacterias();
Console.WriteLine("\nNumber of bacterias to be parsed to database: {0}\n", newbacteriaspath.Count);
Console.WriteLine("Press any key to initiate the parsing");
Console.ReadKey();
Console.WriteLine("Loading newbacterias to database...");
foreach (var bacteria in newbacteriaspath)
{
Console.WriteLine("Parsing .gbff file [{0}/{1}]", i, newbacteriaspath.Count);
List <ISequence> sequences = new List <ISequence>();
ISequenceParser parser = new Bio.IO.GenBank.GenBankParser();
using (parser.Open(bacteria))
{
sequences = parser.Parse().ToList();
}
int j = 1;
foreach (var sequence in sequences)
{
Console.WriteLine("\tParsingSequence [{0}/{1}]", j, sequences.Count);
parse_to_database(sequence);
j++;
}
Console.WriteLine();
append_new_path(bacteria);
i++;
prokaryote_id = 0;
}
}
catch (Exception ex)
{
Console.WriteLine("\nError occured: " + ex.Message);
}
finally
{
if (i - 1 == newbacteriaspath.Count && newbacteriaspath.Count != 0)
{
Console.WriteLine("\nDatabase Updated Successfully");
}
else
{
Console.WriteLine("\nDatabase is not Updated");
}
}
}
//this functiion parses the data from .gbff file
private void extract_sequences()
{
ISequenceParser parser = new Bio.IO.GenBank.GenBankParser();
//Console.WriteLine(path);
using (parser.Open(this.path))
{
this.sequences = parser.Parse().ToList();
}
}
public void GenBankFormatterValidateReadAndWriteMultipleDBLinks()
{
// Create a Sequence with all attributes.
// parse and update the properties instead of parsing entire file.
string tempFileName = Path.GetTempFileName();
ISequenceParser parser1 = new GenBankParser();
using (parser1.Open(_genBankFile_WithMultipleDBLines))
{
var orgSeq = parser1.Parse().First();
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(tempFileName))
{
formatter.Format(orgSeq);
formatter.Close();
}
}
var same = CompareFiles(tempFileName, _genBankFile_WithMultipleDBLines);
File.Delete(tempFileName);
Assert.IsTrue(same);
ApplicationLog.WriteLine("GenBank Formatter: Successful read->write loop");
}
