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

/**
 * Class that manages the whole program
 * @author Gard Thomassen
 * @see Invoke
 * @see PromoterSearchManager
 * @see TerminatorSearchManager
 * @see CandidateComputer
 * @see ResultPrinter
 */

public class ProgramManager {
    
  
    boolean [] consensuses;
    Vector promoterCandidate = new Vector(10,10); 
    Vector terminatorCandidate = new Vector(10,10); 
    Vector ncRNACandidates = new Vector(10,10);
    PromoterSearchManager promoter;
    TerminatorSearchManager terminator;
    SeqTools tools = new SeqTools();
    CandidateComputer candidateComp;
    Vector promoterScore = new Vector(10,10);
    Sequence sequence, reversedCompliment;
    String fileName;
    SequenceIterator seqReader;
    double thresholds [] ;
     
    /**
     * Constructor ProgramManager
     * Establishes connection between pointers and parameters
     * @param c an array with the consensuses that should be searched for
     * @param f the name of the inputfile
     * @param s a sequence iterator connected to the inputfile
     * @param t an array with the thresholds to the given consensuses
     */

    protected ProgramManager(boolean [] c,String f, SequenceIterator s, double [] t){
	consensuses = c;
	fileName = f;
	seqReader = s;
	thresholds = t;
    }
    
    /**
     * This method controls the entire program, first thing is to establish the scoretables for the
     * promoters
     * Next is to read one and one FASTA format sequnce at the time via the FASTA_Reader 
     * Then it creates an object of the 
     * PromoterSearchManager, and calls the function in this object that
     * searches promoters, and puts them in the promoterCandidates Vector.
     * then the same happens for the terminators.
     * Then the candidate vectors are sent to an object of the CandidateComputer class, 
     * the final ncRNA candidates are stored in the vector ncRNACandidates
     * Last thing is to print the results via a ResultPrinter object.
     */
        
    public void start_ncRNAfinder()throws Exception{

	boolean more = true;
	
	PromoterScoreManager promoScoreManager = new PromoterScoreManager(promoterScore, consensuses);
		
	promoter = new PromoterSearchManager(promoterCandidate, promoterScore, thresholds);
	terminator = new TerminatorSearchManager(terminatorCandidate);
	candidateComp = new CandidateComputer(promoterCandidate, terminatorCandidate, ncRNACandidates);
    	
	int z = 0;
	System.out.println("The program is processing your FASTA file, please wait ..");
	try{
	    while(seqReader.hasNext()){
		sequence = seqReader.nextSequence();
		System.out.print(".");
		//searching the sequence
		promoter.startSearch(sequence);
		terminator.startSearch(sequence);
	
		//compute the ncRNA candidates
		candidateComp.computeCandidates();
		
		//revers complimenting the sequence
		reversedCompliment = sequence;
		reversedCompliment = tools.reverseCompliment(reversedCompliment);

		//searching the reverse compliment of the sequence
		promoter.startSearch(reversedCompliment);
	    	terminator.startSearch(reversedCompliment);

		//compute the ncRNA candidates
		candidateComp.computeCandidates();
		
	    }//end while(more)
	}
	catch(Exception e){
	    System.err.println("Error occured while reading FASTA input file");
	}
	//print results
	System.out.println("Computing and printing candidates to file, pleas wait");
	promoter.writePromoterCandidatesToFile();
	terminator.printTermCandidatesToFile();
	ResultPrinter printer = new ResultPrinter(ncRNACandidates, fileName);
	printer.printAllncRNACandidates();
		
    

     }//end start_ncRNAfinder 

}//end class ProgramManager