Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

[jalview.git] / src / jalview / api / FinderI.java

diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index a1a3efd..71b35ef 100644 (file)
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -1,7 +1,26 @@
+/*
+ * 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;
@@ -16,7 +35,7 @@ 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 <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().
    * 
@@ -25,26 +44,25 @@ public interface FinderI
    * @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