package jalview.api;

import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;

import java.util.List;

/**
 * An interface for searching for a pattern in an aligment
 */
public interface FinderI
{

  /**
   * Performs a find for the given search string (interpreted as a regular
   * expression). Search may optionally be case-sensitive, and may optionally
   * including match in sequence description (sequence id is always searched).
   * If the viewport has an active selection, then the find is restricted to the
   * selection region. Sequences matched by id or description can be retrieved
   * by getIdMatches(), and matched residue patterns by getSearchResults().
   * 
   * @param theSearchString
   * @param caseSensitive
   * @param searchDescription
   * @return
   */
  void findAll(String theSearchString, boolean caseSensitive,
          boolean searchDescription);

  /**
   * Finds the next match for the given search string (interpreted as a regular
   * expression), starting from the position after the last match found. Search
   * may optionally be case-sensitive, and may optionally including match in
   * sequence description (sequence id is always searched). If the viewport has
   * an active selection, then the find is restricted to the selection region.
   * Sequences matched by id or description can be retrieved by getIdMatches(),
   * and matched residue patterns by getSearchResults().
   * 
   * @param theSearchString
   * @param caseSensitive
   * @param searchDescription
   * @return
   */
  void findNext(String theSearchString, boolean caseSensitive,
          boolean searchDescription);

  /**
   * Returns the (possibly empty) list of sequences matched on sequence name or
   * description
   * 
   * @return
   */
  List<SequenceI> getIdMatches();

  /**
   * Answers the search results (possibly empty) from the last search
   * 
   * @return
   */
  SearchResultsI getSearchResults();

}