code: public void setBlastFromToPosition(int start, int end) {
  		if (start >= end) {
  			throw new IllegalArgumentException("Start index must be less than end index");
  		}
  		setAlignmentOption(QUERY_FROM, String.valueOf(start));
  		setAlignmentOption(QUERY_TO, String.valueOf(end));
  	}
docs: Sets the QUERY_FROM and QUERY_TO parameters to be use by blast. Do not use if you want to use the whole sequence.<br/>
  Blastall equivalent: -L
  
  @param start QUERY_FROM parameter
  @param end QUERY_TO parameter