X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFinderI.java;h=697072b3d1ee27ee596ed5fc823f6a840f34c6c9;hb=d42b7588a34477b24ce97ba75788536e74e6cf86;hp=d74d87906a6074010c52ee4231af8a0feed0d61d;hpb=b7014049e421026d0f2d57179af9688472cd78f2;p=jalview.git

diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index d74d879..697072b 100644
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -1,10 +1,30 @@
+/*
+ * 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
  */
@@ -14,10 +34,10 @@ public interface FinderI
   /**
    * 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
@@ -29,33 +49,37 @@ public interface FinderI
    * @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
@@ -72,4 +96,6 @@ public interface FinderI
    */
   SearchResultsI getSearchResults();
 
+  void setFeatureRenderer(FeatureRenderer featureRenderer);
+
 }
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