package jalview.util;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

public class DnaUtils
{

  /**
   * Parses an ENA/GenBank format location specifier and returns a list of
   * [start, end] ranges. Returns null if not able to parse.
   * 
   * @param location
   * @return
   * @see http://www.insdc.org/files/feature_table.html#3.4
   */
  public static List<int[]> parseLocation(String location)
  {
    if (location.startsWith("join("))
    {
      return parseJoin(location);
    }
    else if (location.startsWith("complement("))
    {
      return parseComplement(location);
    }
    String errorMessage = "Unable to process location specifier: "
            + location;
    if (location.startsWith("order("))
    {
      System.err.println(errorMessage);
      return null;
    }

    /*
     * try to parse m..n (or simply m)
     */
    String[] range = location.split("\\.\\.");
    if (range.length == 1 || range.length == 2)
    {
      try
      {
        int start = Integer.valueOf(range[0]);
        int end = range.length == 1 ? start : Integer.valueOf(range[1]);
        return Collections.singletonList(new int[] { start, end });
      } catch (NumberFormatException e)
      {
        /*
         * could be a location like <1..888 or 1..>888
         */
        System.err.println(errorMessage);
        return null;
      }
    }
    else
    {
      /*
       * could be a location like 102.110 or 123^124
       */
      System.err.println(errorMessage);
      return null;
    }
  }

  /**
   * Parses a complement(locationSpec) into a list of start-end ranges
   * 
   * @param location
   * @return
   */
  static List<int[]> parseComplement(String location)
  {
    /*
     * take what is inside complement()
     */
    if (!location.endsWith(")"))
    {
      return null;
    }
    String toComplement = location.substring("complement(".length(),
            location.length() - 1);
    List<int[]> ranges = parseLocation(toComplement);
    if (ranges == null)
    {
      /*
       * something bad in there
       */
      return null;
    }

    /*
     * reverse the order and direction of ranges
     */
    Collections.reverse(ranges);
    for (int[] range : ranges)
    {
      int temp = range[0];
      range[0] = range[1];
      range[1] = temp;
    }
    return ranges;
  }

  /**
   * Parses a join(loc1,loc2,...,locn) into a list of start-end ranges
   * 
   * @param location
   * @return
   */
  static List<int[]> parseJoin(String location)
  {
    List<int[]> ranges = new ArrayList<int[]>();

    /*
     * take what is inside join()
     */
    if (!location.endsWith(")"))
    {
      return null;
    }
    String joinedLocs = location.substring("join(".length(),
            location.length() - 1);
    String[] locations = joinedLocs.split(",");
    for (String loc : locations)
    {
      List<int[]> range = parseLocation(loc);
      if (range == null)
      {
        /*
         * something bad in there
         */
        return null;
      }
      else
      {
        ranges.addAll(range);
      }
    }
    return ranges;
  }

}