+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.api;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.util.List;
* 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 <code>selection</code> is not null, then the find is restricted to the
+ * 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 searchDescription
* @return
*/
- void findAll(String theSearchString, SequenceGroup selection,
- boolean caseSensitive, boolean searchDescription);
+ 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
- * <code>selection</code> is not null, 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().
+ * 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 selection
* @param caseSensitive
* @param searchDescription
* @return
*/
- void findNext(String theSearchString, SequenceGroup selection,
- boolean caseSensitive, boolean searchDescription);
+ void findNext(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or