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

/** 
 * Class that uses BIOJAVA to read FASTA file(s)
 * @author Gard Thomassen
 * @see ProgramManager
 * @see ResultPrinter
 * @see Control
 * @see Interaction
*/

public class FASTA_Reader{
    
    Sequence seq;
    BufferedReader br;
    SequenceIterator stream;


    /**
     * method that enables reading of the DNA strings
     * in a FASTA format, through the stream
     * Method that uses biojava package to read FASTA file
     * @param fileName the filename that should be read
     * return SequenceIterator
     */
    
    public SequenceIterator readFASTA(String fileName) throws Exception {
	

	    // Set up sequence iterator
	    br = new BufferedReader(new FileReader(fileName));
	    stream = SeqIOTools.readFastaDNA(br);
	    return stream;

    }//end readFASTA
}//end Class FASTA_Reader