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 ); }