From 1dabd11f09a42682d2b62d0a7bfccfd4114e07d9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 14 May 2010 14:37:10 +0000
Subject: [PATCH] partial patch for * JAL-466 allows finder to be instantiated
 for an explicit alignment panel and viewport.

---
 src/jalview/gui/Finder.java |   27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e211e3e..5fc2a01 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -58,6 +58,15 @@ public class Finder extends GFinder
    */
   public Finder()
   {
+    this(null, null);
+    focusfixed = false;
+  }
+
+  public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+  {
+    av = viewport;
+    ap = alignPanel;
+    focusfixed = true;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -97,12 +106,28 @@ public class Finder extends GFinder
   }
 
   /**
-   * gets the topmost alignment window and sets av and ap accordingly
+   * do we only search a given alignment view ?
+   */
+  private boolean focusfixed;
+
+  /**
+   * 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
    */
   boolean getFocusedViewport()
   {
+    if (focusfixed || Desktop.desktop == null)
+    {
+      if (ap != null && av != null)
+      {
+        return true;
+      }
+      // we aren't in a desktop environment, so give up now.
+      return false;
+    }
     // now checks further down the window stack to fix bug
     // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-- 
1.7.10.2