import java.util.*;
import java.io.*;
import java.util.*;

/**
 * Class Interaction is the class that manages the user interaction.
 * All input parameters are given to class Control
 * @author Gard Thomassen
 * @see Invoke
 * @see Control
 */

public class Interaction{
    
    Control control;
    boolean correct = true; 
    String input;
    BufferedReader stdin;
    
    /**
     * Cosntructor Interaction is used to create an instance of the Control class, 
     * this object is used to store all data from the user in. The object is returned 
     * to class Invoke by the method interact.
     */


    Interaction(){
	control = new Control();
	try{
	    stdin = new BufferedReader(new InputStreamReader(System.in));
	}
	catch(Exception e){
	    System.out.println("Something wrong whiel creating input reader");
	    System.exit(1);
	}
    }

    /**
     * Method interact asks the user for the name of the inputfile.
     * Inputfile are given to the Control class
     * Method also invokes the two methods that asks the user which consensuses to 
     * search for, and what thresholds to use.
     * return an instance of the Control class
     */

    public Control interact(){
	
	try{
	    
	    while(correct) {
		System.out.println("Enter the name and location of the FASTA formatted file you wish to search");
		System.out.println("Type 'q' to exit the program");
		input = stdin.readLine();
		if(input.equals("q"))
		    System.exit(0);
		else{ 
		    if(control.createSeqIterator(input))
			correct = false;
		    else
			System.out.println("Wrong filename or path to the FASTA formatted file");
		}
	    }
	    chooseConsensus();
	    setThresholds();
	}    
	catch(Exception e){
	    System.out.println("Something went wrong while choosing search parameters");
	}
	
	return control;
	
    }//end interact
	
    /**
     * Method chooseConsensus asks the user which of the consensuses to 
     * search for. User input is stored in an instance of the Control class
     */



    public void chooseConsensus()throws Exception{
	
	System.out.println("Now you will be prompted to choose whether or not to include different consensus sequences in the search");
	System.out.println("Type 'q' to exit the program");
	System.out.println("Include consensus sequecence to the region recognized by sigma 70, accoring to Pedersen et al. and Ussery (y or n}");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[0] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else 
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	}
	
	System.out.println("Include consensus sequecence to the region recognized by sigma 32, accoring to Pedersen et al. and Ussery (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[1] = true; 
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include consensus sequecence to the region recognized by sigma 54, accoring to Pedersen et al. and Ussery (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[2] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include consensus sequecence to the region recognized by sigma 38, accoring to Pedersen et al. and Ussery (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[3] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include non sigma specific consensus sequecence accoring Lisser and Margalit (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[4] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include consensus sequecence to the region recognized by sigma 70, accoring to regulonDB (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[5] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else 
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include consensus sequecence to the region recognized by sigma 32, accoring to Pedersen et al. and Ussery (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[6] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
	System.out.println("Include consensus sequecence to the region recognized by sigma 24, accoring to Pedersen et al. and Ussery (y or n)");
	correct = true;
	while(correct){
	    input = stdin.readLine();
	    if(input.equals("q"))
		System.exit(0);
	    else if(input.equals("y")){
		control.consensuses[7] = true;
		correct = false;
	    }
	    else if(input.equals("n"))
		correct = false;
	    else
		System.out.println("Type 'y' or 'n' then press 'ENTER'");
	    
	}
    }//end chooseConsensus
 
    /**
     * Method setThresholds  asks the user which thresholds to use accoring to the 
     * consensuses chosen in method chooseConsensus
     */


    private void setThresholds()throws Exception{
	int n = 0;
	double threshold;
	if(control.consensuses[0]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 70 consensus sequence from Pedersen et al. and Ussery");
		System.out.println("95 % is recommended , min and max are 87-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(86 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}
	
	if(control.consensuses[1]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 32 consensus sequence from Pedersen et al and Ussery");
		System.out.println("82 % is recommended , min and max are 75-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(74 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}

	if(control.consensuses[2]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 54 consensus sequence from Pedersen et al and Ussery");
		System.out.println("93 % is recommended , min and max are 85-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(84 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}


	if(control.consensuses[3]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 38 consensus sequence from Pedersen et al and Ussery");
		System.out.println("91 % is recommended , min and max are 80-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(79 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}


	if(control.consensuses[4]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the non sigma specific  consensus sequence from Lisser and Margalit");
		System.out.println("88 % is recommended , min and max are 77-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(76 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}

	if(control.consensuses[5]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 70 consensus sequence from the regulon database");
		System.out.println("95 % is recommended , min and max are 87-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(86 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}

	if(control.consensuses[6]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 32 consensus sequence from the regulon database");
		System.out.println("83 % is recommended , min and max are 75-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		   System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(74 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		   control.thresholds[n+1] = threshold;
		   n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}
	if(control.consensuses[7]){
	    correct = true;
	    while(correct){
		System.out.println("Type your threshold for the sigma 24 consensus sequence from the regulon database");
		System.out.println("85 % is recommended , min and max are 75-100, type 'q' to exit");
		input = stdin.readLine();
		if(input.equals("q"))
		    System.exit(0);
		
		threshold =  Integer.parseInt(input);
		if(74 < threshold && threshold <= 100){
		    control.thresholds[n] = threshold;
		    control.thresholds[n+1] = threshold;
		    n = n+2;
		    correct = false;
		}
		else{
		    System.out.println("Wrong format of threshold value, or value set to low or to high");
		}
	    }
	}
    }//end setThresholds

}//end class