partial patch for * JAL-466

allows finder to be instantiated for an explicit alignment panel and viewport.

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5aed688..762aab2 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -109,8 +109,9 @@ public class Finder extends GFinder
   private boolean focusfixed;
 
   /**
-   * checks that av and ap are valid, and if not,
-   * gets the topmost alignment window and sets av and ap accordingly
+   * if !focusfixed and not in a desktop environment, checks that av and ap are
+   * valid. Otherwise, gets the topmost alignment window and sets av and ap
+   * accordingly
    * 
    * @return false if no alignment window was found
    */