- * 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.