package oligo3;
import java.io.File;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.List;
/** Types and methods for safely opening an input file for reading lines of text.
 *  Note: Don't forget to close the BufferedReader stream after using this class.
 */
public class InputFile {

    public static File f;
    private static FileReader fr;
    public static BufferedReader br;

/**Check and open file and create FileReader and BufferedReader.
 * @param String filename contains no the path to the file to be opened.
 */
    public static boolean OpenOkay (String dir, String filename)
      throws FileNotFoundException, IOException {
      f = new File(dir, filename);
      if (f == null) {
         throw new IllegalArgumentException("File should not be null.");
      } else if (!f.exists()) {
         throw new FileNotFoundException (filename + ": File does not exist.");
      } else if (!f.isFile()) {
         throw new IllegalArgumentException(filename + ": Is a directory, not a file.");
      } else if (!f.canRead()) {
         throw new IllegalArgumentException(filename + ": File cannot be read.");
      }
      // Continue checking
      try {
        fr = new FileReader(f);
        br = new BufferedReader(fr);
      } catch (FileNotFoundException e) {
        System.err.println("File not found: " + e.getMessage());
      } catch (IOException e) {
        System.err.println("I/O File Read Error: " + e.getMessage());
      }
      return br.ready(); // Tells whether this stream is ready to be read.
    }

    public static String[] getArray() throws IOException {
      // generic and type-safe instantiation
      List<String> lines = new ArrayList<String>();
      String line = null;
      while ((line = br.readLine())!= null) {
         lines.add(line.trim());
      }
      if (br != null) br.close();
      return lines.toArray(new String[lines.size()]);
    }
}