+/*
+ * 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 java.util.List;
+
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
-import java.util.List;
-
/**
* An interface for searching for a pattern in an aligment
*/
/**
* 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
* @param theSearchString
* @param caseSensitive
* @param searchDescription
+ * @param searchFeatureDesc
* @param ignoreHidden
* @return
*/
void findAll(String theSearchString, boolean caseSensitive,
- boolean searchDescription, boolean ignoreHidden);
+ boolean searchDescription, boolean searchFeatureDesc,
+ 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.
+ * 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 searchFeatureDesc
* @param ignoreHidden
* @return
*/
void findNext(String theSearchString, boolean caseSensitive,
- boolean searchDescription, boolean ignoreHidden);
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or
*/
SearchResultsI getSearchResults();
+ void setFeatureRenderer(FeatureRenderer featureRenderer);
+
}
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