*/
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
*/
* 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 searchFeatureDesc
+ * @param ignoreHidden
* @return
*/
void findAll(String theSearchString, boolean caseSensitive,
- boolean searchDescription);
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden);
/**
* Finds the next match for the given search string (interpreted as a regular
* 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 searchFeatureDesc
+ * @param ignoreHidden
* @return
*/
void findNext(String theSearchString, boolean caseSensitive,
- boolean searchDescription);
+ 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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