JAL-1370 allow show unconserved to reflect differences from the current reference...

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index a5dfb83..89289c0 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * 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 
@@ -146,7 +146,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
     scrollToVisible();
   }
 
@@ -342,31 +342,35 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       keyboardNo1.append(value);
     }
   }
-
   int getKeyboardNo1()
   {
-    if (keyboardNo1 == null)
-      return 1;
-    else
+    try {
+    if (keyboardNo1 != null) 
     {
       int value = Integer.parseInt(keyboardNo1.toString());
       keyboardNo1 = null;
       return value;
     }
+    } catch (Exception x)
+    {}
+    keyboardNo1 = null;
+    return 1;
   }
 
   int getKeyboardNo2()
   {
-    if (keyboardNo2 == null)
-      return 1;
-    else
-    {
+    try {
+    if (keyboardNo2!=null){
       int value = Integer.parseInt(keyboardNo2.toString());
       keyboardNo2 = null;
       return value;
     }
+    } catch (Exception x)
+    {}
+    keyboardNo2 = null;
+    return 1;
   }
-
+  
   void setStatusMessage(SequenceI sequence, int res, int seq)
   {
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "