/**
 * Options read from the command line. This class provides a convenient way to pass options to any method.
 */
package oligo3;
import java.io.File;

public class ParseOptions {
    /*
     * Parse command line arguments.
     */
    static boolean flag = false;

    public static boolean parseCmdLine(String[] args) {
      // Check and return command line parsing status
      if (args.length > 0) {
        try {
          for (int i = 0; i < args.length; i++) {
            // Parse and validate command-line arguments
            // Input filename has format requirements
            if (args[i].startsWith("-p")) {
               Params.parameters_file = args[i].equals("-p")?args[++i]:args[i].substring(2);
               if (!Params.parameters_file.matches("^\\w[\\w\\s\\(\\)\\.,-]*[\\w\\)]*$")) {
                  System.out.println(Params.parameters_file + ": Invalid file name!");
                  System.exit(1);
               }
            } else if (args[i].startsWith("-f")) {
              Params.input_genes_file = args[i].equals("-f")?args[++i]:args[i].substring(2);
              if (!Params.input_genes_file.matches("^\\w[\\w\\s\\(\\)\\.,-]*[\\w\\)]*$")) {
                 System.out.println("\n" + Params.input_genes_file + ": Invalid file name!\n");
                 System.exit(1);
              } else {
                flag = true;
              }
            } else if (args[i].equals("-h")) {
               System.out.println(Params.usage);
               System.exit(1);
            } else {
               System.out.println("Unknown arguments: " + args[i]);
               System.out.println(Params.usage);
               System.exit(1);
            }
          }
        } catch (ArrayIndexOutOfBoundsException e) {
          System.err.println("No parameter found after "+args[Integer.parseInt(e.getMessage())-1]);
          System.exit(1);
        }
      } else {
         //Use default parameters without using parameters_file
         //The input file must be named "input-genes.ffn" and placed in user's
         //current working directory and all output files will be placed there
         //return false;
      }
      return true;
    }
}