JAL-1270 Desktop.instance is null during headless jalview tests

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9e99bae..94d5ca8 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,20 +1,21 @@
 /*
- * 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
+ * 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
+ *  
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
+
 package jalview.gui;
 
 import java.util.*;
@@ -128,8 +129,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
-      ssm = StructureSelectionManager
-              .getStructureSelectionManager(Desktop.instance);
+      ssm = av.getStructureSelectionManager();
       ssm.addStructureViewerListener(this);
       ssm.addSelectionListener(this);
     }
@@ -306,7 +306,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
     scrollToVisible();
   }
 
@@ -517,26 +517,31 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   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;
   }
 
   /**