code: private void prepareReader(BufferedReader fileReader, String fileId)
  	{
  
  		switch (fileType)
  		{
  		case EMBL:
  			EmblEntryReader emblReader = new EmblEntryReader(	fileReader,	EmblEntryReader.Format.EMBL_FORMAT,fileId);
  			emblReader.setCheckBlockCounts(lineCount);
  			reader = emblReader;
  			break;
  		case GENBANK:
  			reader = new GenbankEntryReader(fileReader,fileId);
  			break;
  		case GFF3:
  			reader = new GFF3FlatFileEntryReader(fileReader);
  			break;
  		case FASTA:
  			reader = new FastaFileReader(new FastaLineReader(fileReader));
  			break;
  		case AGP:
  			reader= new AGPFileReader(new AGPLineReader(fileReader));
  			break;
  		default:
  			System.exit(0);
  			break;
  		}
  	}
docs: Prepare reader.
  
  @param fileReader
  the file reader
  @param fileId
  the file name