package jalview.util;

import java.io.IOException;
import java.util.Scanner;

/**
 * This class contains the brain of the analyser program, and contains a number
 * of commands for the processing of data.
 * 
 * @author TZVanaalten
 *
 */

public class ProbabilityAnalyserKickstarter
{

  public static void main(String[] args)
          throws IOException, InterruptedException
  {

    // this does all of the processing
    HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();

    boolean running = true;
    System.out.println("ACTIVATED");
    while (running)
    {
      Scanner keyboard = new Scanner(System.in);
      String command = keyboard.nextLine();

      Scanner inputScanner = new Scanner(command);
      // prints family to console. Syntax is printFam <index>
      if (command.indexOf("printFam") > -1)
      {
        try
        {
          inputScanner.next();
          int index = inputScanner.nextInt();
          analyser.printFam(index);
          continue;
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }

      }
      // prints HMM to console. Syntax is printHMM <index>
      if (command.indexOf("printHMM") > -1)
      {
        try
        {
        inputScanner.next();
        int index = inputScanner.nextInt();
        analyser.printHMM(index);
        continue;
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
      }
      // prints family to file in current folder. Syntax is exportFam <index>.
      if (command.indexOf("exportFam") > -1)
      {
        try
        {
        inputScanner.next();
        int index = inputScanner.nextInt();
          String location = inputScanner.next();
          analyser.exportFam(index, location);
        continue;
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
      }
      // prints HMM to file in current folder. Syntax is exportHMM <index>.
      if (command.indexOf("exportHMM") > -1)
      {
        try
        {
        inputScanner.next();
        int index = inputScanner.nextInt();
          String location = inputScanner.next();
          analyser.exportHMM(index, location);
        continue;
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
      }
      // Processes data. Syntax is run <number of loops> <increments>. The
      // number loops specifies the number of increments the program will run.
      // After each increment, the data stored currently in the program is
      // exported and re-read back into the program. This is to ensure that the
      // program can be terminated without losing a large quantity of data. The
      // increment is the number of families read per 'save'.
      if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
      {
        try
        {

        inputScanner.next();

        int loops = inputScanner.nextInt();
        int increments = inputScanner.nextInt();
        boolean keepRaw = inputScanner.nextBoolean();

        for (int i = 0; i < loops; i++)
        {
          analyser.run(increments, keepRaw);
          System.out.println("Saved");
        }
        System.out.println("Task completed");
        continue;
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
        continue;
      }
      if ((command.indexOf("runToEnd") > -1))
      {
        try
        {

          inputScanner.next();
          int minCount = inputScanner.nextInt();
          int maxCount = inputScanner.nextInt();
          boolean keepRaw = inputScanner.nextBoolean();
          boolean forClans = inputScanner.nextBoolean();
          analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
          System.out.println("Task completed");
        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
        continue;
      }
      // terminates program. Syntax is terminate.
      if (command.indexOf("terminate") > -1)
      {
        running = false;
        continue;
      }
      // clears files in current directory (Only a specific set of files).
      // Syntax is clear.
      if (command.indexOf("clear") > -1)
      {
        analyser.clear();
        continue;
      }
      // changes current directory. Syntax is cd <directory>
      if (command.indexOf("cd") > -1)
      {
        try
        {
        inputScanner.next();
        analyser.setFolder(inputScanner.next());
        } catch (Exception e)
        {
          System.out.println("Command failed");

        }
        continue;
      }

      if (command.indexOf("getFamName") > -1)
      {
        try
        {
        inputScanner.next();
        System.out.println(analyser.getFamilyName(inputScanner.nextInt()));

        } catch (Exception e)
        {
          System.out.println("Command failed");
        }
        continue;
      }
      if (command.indexOf("sortIntoClans") > -1)
      {
        inputScanner.next();
        analyser.sortIntoClans(inputScanner.next());
          continue;

      }
      if (command.indexOf("setFamilies") > -1)
      {
        inputScanner.next();
        analyser.setFamilies(inputScanner.next());
        continue;

      }

      if (command.indexOf("setHMMs") > -1)
      {
        inputScanner.next();
        analyser.setHmms(inputScanner.next());
        continue;

      }

      if (command.indexOf("alignWithinClans") > -1)
      {
        inputScanner.next();
        String export = inputScanner.next();
        String clans = inputScanner.next();
        analyser.alignWithinClan(export, clans);
        continue;

      }

      System.out.println("Unrecognised command");
    }




  }

}