package oligo3;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.io.IOException;
import java.io.FileNotFoundException;
/**Types and method for safely opening an output file for writing lines of text.
 * Note: Don't forget to close the BufferedWriter stream after using this class.
 */
public class OutputFile {

    public static File f;
    private static FileWriter fw;
    public static PrintWriter pw;
    public static PrintWriter genes;
    public static PrintWriter overlaps;
    public static PrintWriter stats;
    public static PrintWriter tags;

/**Check and open file and create FileWriter and BufferedWriter.
 * @param String filename contains no the path to the file to be opened.
 */
    public static boolean WriteOkay(String dir, String filename, boolean append)
      throws FileNotFoundException, IOException {
      //FileWriter always assumes that default encoding is Okay!
      f = new File(dir, filename);
      if (f == null) {
         throw new IllegalArgumentException("File should not be null.");
      } else if (!f.exists()) {
         System.out.println("\n" + f.getName() + ": File does not exist.");
         if (f.createNewFile()) {
            System.out.println("Successfully created the file: " + f.getName());
         } else {
            System.out.println("Unable to create the file " + f.getName());
         }
      }
      // Check the existing or freshly created file
      if (!f.isFile()) {
         throw new IllegalArgumentException(f + ": Is a directory, not a file.");
      } else if (!f.canWrite()) {
         throw new IllegalArgumentException(f + ": File cannot be written.");
      }
      // Continue checking
      try {
        fw = new FileWriter(f, append);
	pw = new PrintWriter(fw);
      } catch (IOException e) {
        System.err.println("I/O File Write Error: " + e.getMessage());
        System.exit(1);
      } catch (Exception e) {
        System.err.println("Print Write Error: " + e.getMessage());
        System.exit(1);
      }
      return f.canWrite();
    }

    public static void createOutFiles() throws IOException {
      // Use overwrite mode to clear existing file contents.
      if (WriteOkay(Params.output_files_dir, Params.output_genes_file, false)) pw.close();
      if (WriteOkay(Params.output_files_dir, Params.out_overlaps_file, false)) pw.close();
      if (WriteOkay(Params.output_files_dir, Params.ORF_stats_file, false)) pw.close();
      if (WriteOkay(Params.output_files_dir, Params.ORF_tags_file, false)) pw.close();
      // Stay append mode after clearing existing file contents.
      if (WriteOkay(Params.output_files_dir, Params.output_genes_file, true)) genes = pw;
      if (WriteOkay(Params.output_files_dir, Params.out_overlaps_file, true)) overlaps = pw;
      if (WriteOkay(Params.output_files_dir, Params.ORF_stats_file, true)) stats = pw;
      if (WriteOkay(Params.output_files_dir, Params.ORF_tags_file, true)) tags = pw;
    }
}