/**
* 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().
+ * 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().
+ * <p>
+ * 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).
+ * <p>
+ * 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 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.
+ * 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().
+ * <p>
+ * 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 searchDescription, boolean ignoreHidden);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or