JAL-1161 conditional parameters for controlling clipping

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index eef4b62..7722461 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -115,9 +115,9 @@ public class Finder extends Panel implements ActionListener
 
   void doSearch(boolean findAll)
   {
-    if (jalview.bin.JalviewLite.currentAlignFrame != null)
+    if (ap.av.applet.currentAlignFrame != null)
     {
-      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+      ap = ap.av.applet.currentAlignFrame.alignPanel;
       av = ap.av;
     }
     createNewGroup.setEnabled(false);
@@ -167,24 +167,31 @@ public class Finder extends Panel implements ActionListener
       resIndex = -1;
       seqIndex = 0;
     }
-    if (findAll)
+    else
     {
-      String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
-              : "";
-      if (idMatch.size() > 0 && searchResults != null
-              && searchResults.getSize() > 0)
+      if (findAll)
       {
-        message += " and ";
+        String message = (idMatch.size() > 0) ? "" + idMatch.size()
+                + " IDs" : "";
+        if (idMatch.size() > 0 && searchResults != null
+                && searchResults.getSize() > 0)
+        {
+          message += " and ";
+        }
+        if (searchResults != null)
+        {
+          message += searchResults.getSize() + " subsequence matches.";
+        }
+        ap.alignFrame.statusBar.setText("Search results: " + searchString
+                + " : " + message);
+
       }
-      if (searchResults != null)
+      else
       {
-        message += searchResults.getSize() + " subsequence matches.";
+        // TODO: indicate sequence and matching position in status bar
+        ap.alignFrame.statusBar.setText("Found match for " + searchString);
       }
-      ap.alignFrame.statusBar.setText("Search results: " + searchString
-              + " : " + message);
-
     }
-
   }
 
   Label jLabel1 = new Label();