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


/**
 * Class TerminatorSearchManager, searches for  
 * terminators, stores candidates in a
 * terminatorCandidates Vector
 * @author Gard Thomassen
 * @see ProgramManager
 * @see TerminatorSearcher
 * @see TerminatorCandidate
*/

public class TerminatorSearchManager{
    
    Vector termCand;
    TerminatorSearcher termSearcher;
    PrintWriter outTerm;
    
    /**
     * Constructor that creates a pointer to the vector
     * of terminator candidates. It also creates a Printwriter
     * for where to print the TerminatorCandiates
     * @param t the vector holding all TerminatorCandiates
     */

    protected TerminatorSearchManager(Vector t){
	termCand = t;
	//creating outputStream
	try{
	    outTerm = new PrintWriter(new BufferedWriter(new FileWriter("TerminatorCandidates.txt")));
	}
	catch(IOException e){
	    System.err.println("Trouble while creating output stream for terminator candidates");
	}
	
    }

     /**
     * This method initiates the overall search by creating a TerminatorSearcher
     * object and then it fills the TerminatorCandidate vector by calling the 
     * TermiantorSearchers method startTermSearch.
     * @param s the sequence to search for terminators
     */

    public void startSearch(Sequence s){
	termSearcher = new TerminatorSearcher();
	termCand.addAll(termSearcher.startTermSearch(s));
    }
    

     /**
     * This method prints all Terminator candidate info to a file
     * specified by the FileWriter created in this class' constructor.
     */


    public void printTermCandidatesToFile(){
        TerminatorCandidate cand;
	int i = 0;

	//iterate through all Terminator Candidates
	while(i < termCand.size()){
	    cand = (TerminatorCandidate)termCand.elementAt(i);
	    //writing data to file
	    cand.writeTerminatorCandidatesToFile(outTerm, i);
	    i++;
	    
	}//end while
	System.out.println("Located : " + termCand.size() + " terminator candidates");
	outTerm.close();

    }//end PrintterminatorCandidatesToFile
}//end class TerminatorSearcher