private void Create(string RegexFile, string PssmFile, string DatabaseFile, string VariantsFile, string OutputDir, bool grouping)
{
string line;
// regex
UnixCfg rd = new UnixCfg(RegexFile);
line = rd.ReadUnixLine();
if (line == null)
{
throw new ApplicationException("Empty regex");
}
rd.Close();
if (PssmFile.Length > 0)
{
mRegex = new WregexManager(line, new PSSM(PssmFile), grouping);
}
else
{
mRegex = new WregexManager(line, grouping);
}
// Fasta
mSeqs = new List <Fasta>();
if (DatabaseFile.Contains(".fasta"))
{
LoadFasta(DatabaseFile);
}
else
{
SortedList <string, List <Variant> > list = null;
if (VariantsFile.Length != 0)
{
list = LoadVariants(VariantsFile);
}
LoadXml(DatabaseFile, list);
}
// Sort Variants
foreach (Fasta seq in mSeqs)
{
seq.mVariants.Sort();
}
mDataId = Path.GetFileNameWithoutExtension(DatabaseFile);
mOutputDir = OutputDir;
Directory.CreateDirectory(OutputDir);
}
private void Create( string RegexFile, string PssmFile, string DatabaseFile, string VariantsFile, string OutputDir, bool grouping )
{
string line;
// regex
UnixCfg rd = new UnixCfg( RegexFile );
line = rd.ReadUnixLine();
if( line == null )
throw new ApplicationException( "Empty regex" );
rd.Close();
if( PssmFile.Length > 0 )
mRegex = new WregexManager( line, new PSSM(PssmFile), grouping );
else
mRegex = new WregexManager( line, grouping );
// Fasta
mSeqs = new List<Fasta>();
if( DatabaseFile.Contains(".fasta") )
LoadFasta( DatabaseFile );
else {
SortedList<string,List<Variant>> list = null;
if( VariantsFile.Length != 0 )
list = LoadVariants( VariantsFile );
LoadXml( DatabaseFile, list );
}
// Sort Variants
foreach( Fasta seq in mSeqs )
seq.mVariants.Sort();
mDataId = Path.GetFileNameWithoutExtension( DatabaseFile );
mOutputDir = OutputDir;
Directory.CreateDirectory( OutputDir );
}
