import java.io.*;
import java.util.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;


/**
 * Class Control is a class that controls the input parameters  
 * from the user interaction, an instance of this class is delivered 
 * by the INteraction calss to the actual 
 * executing part of the program
 * @author Gard Thomassen
 * @see Invoke
 * @see Interaction
 * @see FASTA_Reader
 */

public class Control{

    FASTA_Reader FASTA_reader;
    SequenceIterator seqReader;
    String fileName;
    
    Control(){
	FASTA_reader = new FASTA_Reader();
    }
 


    /**
     * Boolean method createSeqIterator creates a sequence iterator
     * to the input file specified by the user, this is 
     * done by using the Fasta_reader class.  
     * @param f filename sepcified by the user  
     * return boolean wheter the iterator is created or not.
     * @see Interaction
     */

   
    public boolean createSeqIterator(String f){
	try{
	    fileName = f;
	    seqReader = FASTA_reader.readFASTA(f);
	    return true;
	}
	catch(Exception e){
	    return false;
	}
	
    }

    boolean [] consensuses = new boolean []{false,false,false,false,false,false,false,false};
    double [] thresholds = new double [16];

}