/*
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 */
package oligo3;
import java.io.File;
import java.util.Arrays;
import java.io.IOException;
import java.io.BufferedReader;
import java.io.FilenameFilter;
import java.io.InputStreamReader;
import java.lang.management.ManagementFactory;
/**
 *
 * @author rli
 */
public class RunJob {

    public static String[] files;
    public static String s = "";

    public static void getStdInput() {
      BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
      do {
         System.out.print("Proceed to run ? [y/b/n]: ");
         try {
           s = br.readLine().trim();
         } catch (IOException e) {
           System.err.println("Error: " + e.getMessage());
         }
	 if (s.equalsIgnoreCase("n")) {
            System.out.println("");
            System.exit(1);
         }
      } while (!s.matches("[byBY]"));
      if (s.equalsIgnoreCase("b")) {
         System.out.println("\nPlease type bg to run in the background.");
         Process pr = null;
         String p = "";
         try {
           p = ManagementFactory.getRuntimeMXBean().getName();
           p = p.substring(0, p.indexOf('@'));
         } catch (Exception e) {
           System.err.println("Error: " + e.getMessage());
         }
         try {
           pr = Runtime.getRuntime().exec("kill -STOP " + p);
         } catch (IOException e) {
           System.err.println("Error: " + e.getMessage());
         }
         try {
           pr.waitFor();
         } catch (InterruptedException e) {
           System.err.println("Error: " + e.getMessage());
         }
      }
    }

    public static void runSelectedJob() throws IOException {
      // Transform start codons into Java regex-usable
      Params.ORF_start_codons = Params.ORF_start_codons.toUpperCase().replace(",","|");
      // Selectively execute the program
      switch(Params.input_file_mode) {
        case 1:
          // Get a list of files from parameter file or command line.
          files = Params.input_genes_file.split(",");
          break;
        case 2:
          // Get a list of files from a list file in data directory.
          if (InputFile.OpenOkay(Params.input_files_dir, Params.input_genes_file)) {
            files = InputFile.getArray();
          }
          break;
        case 3:
          // Get a list of files from a directory in this case.
          File d = new File(Params.input_files_dir);
          files = d.list(new FilenameFilter() {
          @Override
          public boolean accept(File dir, String name) {
            return name.toLowerCase().endsWith(".ffn");
          }});
          Arrays.sort(files);
          break;
      }
    }
}