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(). *
* If {@code ignoreHidden} is true, then any residues in hidden columns are * ignored (skipped) when matching, so for example pattern {@code KRT} would * match sequence {@code KRqmT} (where {@code qm} are in hidden columns). *
* Matches of entirely hidden patterns are not returned. Matches that span * hidden regions on one or both sides may be returned. * * @param theSearchString * @param caseSensitive * @param searchDescription * @param ignoreHidden * @return */ void findAll(String theSearchString, boolean caseSensitive, boolean searchDescription, boolean ignoreHidden); /** * 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(). *
* If {@code ignoreHidden} is true, any hidden residues are skipped (matches may
* span them). If false, they are included for matching purposes. In either
* cases, entirely hidden matches are not returned.
*
* @param theSearchString
* @param caseSensitive
* @param searchDescription
* @param ignoreHidden
* @return
*/
void findNext(String theSearchString, boolean caseSensitive,
boolean searchDescription, boolean ignoreHidden);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or
* description
*
* @return
*/
List