update author list in license for (JAL-826)

[jalview.git] / src / jalview / gui / Finder.java

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e211e3e..c758166 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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();
@@ -221,11 +246,14 @@ public class Finder extends GFinder
     {
       String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
               : "";
-      if (idMatch.size() > 0 && searchResults.getSize() > 0)
+      if (searchResults != null)
       {
-        message += " and ";
+        if (idMatch.size() > 0 && searchResults.getSize() > 0)
+        {
+          message += " and ";
+        }
+        message += searchResults.getSize() + " subsequence matches found.";
       }
-      message += searchResults.getSize() + " subsequence matches found.";
       JOptionPane.showInternalMessageDialog(this, message, null,
               JOptionPane.INFORMATION_MESSAGE);
       resIndex = -1;