import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.utils.*;
import org.biojava.bio.seq.impl.RevCompSequence;

/**
 * This class holds a method to manipulate sequences. 
 * The class uses bioJava packages
 * @author Gard Thomassen
 * @see ProgramManager
 */



class SeqTools{
 
    /** this method gets a sequence and return
     * the reverse compliment
     * @param s the sequence to reverse comliment
     * @return the reverse complimented sequence
     */
    
    public Sequence reverseCompliment (Sequence s){
	RevCompSequence reversedSeq = null;	
	
	try{
	reversedSeq = new RevCompSequence(s);
	}
	catch (Exception e){
	    System.err.println("Error whiule reverse comlimenting sequence");
	}
       	reversedSeq.setName(reversedSeq.getName().concat(".reversed"));
	
	return (Sequence) reversedSeq;
    }
}