import java.util.*;

/**
 * A dummy SequenceSearch class, to allow classes using SequenceSearch
 * to compile.  Returns meaningless values with the correct types.
 * Replace with the real GeneDataSearch.
 */
public class GeneDataSearch implements SequenceSearch {

  /**
   * Search through all gene sequences and find matches to the given
   * pattern that have a Hamming distance no more than the given value.
   * Return a Collection containing a SearchResult object for each sequence
   * with at least one sufficiently close match.
   *
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a Collection containing a SearchResult object for each sequence
   *   with matches
   */
  public Collection searchGenesByHammingDistance( String pattern,
                                                  int maxDistance) {
    return null;
  }

  /**
   * Search through all protein sequences and find matches to the given
   * pattern that have a Hamming distance no more than the given value.
   * Return a Collection containing a SearchResult object for each sequence
   * with at least one sufficiently close match.
   *
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a Collection containing a SearchResult object for each sequence
   *   with matches
   */
  public Collection searchProteinsByHammingDistance( String pattern,
                                                     int maxDistance) {
    return null;
  }

  /**
   * Search through all gene sequences and find matches to the given
   * pattern that have an edit distance no more than the given value.
   * Return a Collection containing a SearchResult object for each sequence
   * with at least one sufficiently close match.
   *
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a Collection containing a SearchResult object for each sequence
   *   with matches
   */
  public Collection searchGenesByEditDistance( String pattern,
                                               int maxDistance) {
    return null;
  }

  /**
   * Search through all protein sequences and find matches to the given
   * pattern that have an edit distance no more than the given value.
   * Return a Collection containing a SearchResult object for each sequence
   * with at least one sufficiently close match.
   *
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a Collection containing a SearchResult object for each sequence
   *   with matches
   */
  public Collection searchProteinsByEditDistance( String pattern,
                                                  int maxDistance) {
    return null;
  }

  // Methods that search one sequence of any sort, finding match locations.

  /**
   * Searches a sequence for substrings that match a given pattern, using
   * Hamming distance.  A substring matches if its distance is no more
   * than the given maximum.  Returns the locations of the matches in a
   * List of Integers.  The location is the index in the sequence of the
   * beginning of the substring that was a sufficiently close match.
   *
   * @param sequence - the sequence to search for matches
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a List of Integers containing locations of matches in this
   * sequence
   */
  public List searchOneSequenceByHammingDistance(
                String sequence, String pattern, int maxDistance) {
    return null;
  }

  /**
   * Searches a sequence for substrings that match a given pattern, using
   * edit distance.  A substring matches if its distance is no more
   * than the given maximum.  Returns the locations of the matches in a
   * List of Integers.  The location is the index in the sequence of the
   * beginning of the substring that was a sufficiently close match.
   *
   * @param sequence - the sequence to search for matches
   * @param pattern - the pattern to be used in the distance comparison
   * @param maxDistance - the largest distance that should be accepted
   *   as a match
   * @return a List of Integers containing locations of the matches in this
   * sequence
   */
  public List searchOneSequenceByEditDistance(
                String sequence, String pattern, int maxDistance) {
    return null;
  }

  // Methods that compare strings and return a "distance" that measures
  // how dissimilar the strings are.

  /**
   * Computes the Hamming distance between two strings.
   *
   * @param a - one string to compare
   * @param b - the other string to compare
   * @return the Hamming distance between the two strings
   */
  public int hammingDistance( String a, String b ) {
    return -1;
  }

  /**
   * Computes the edit distance between two strings.
   *
   * @param a - one string to compare
   * @param b - the other string to compare
   * @return the edit distance between the two strings
   */
  public int editDistance( String a, String b ) {
    return -1;
  }

  /**
   * Returns the "version number" of the protein translation procedure.
   * This should be 1 if the class provides the original translation
   * procedure, or 2 if it uses the updated procedure.
   *
   * @return version number of the protein translation procedure
   */
  public int translationVersion() {
    return 0;
  }
}