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fix for JAL-895 - new exampleFile_2_7.jar and logic to upgrade stale default startup...
[jalview.git] / src / jalview / gui / SeqPanel.java
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index a1913a8..968d302
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -33,7 +33,7 @@ import jalview.structure.*;
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
  */
 public class SeqPanel extends JPanel implements MouseListener,
         MouseMotionListener, MouseWheelListener, SequenceListener,
@@ -123,7 +123,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
-      ssm = StructureSelectionManager.getStructureSelectionManager();
+      ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
       ssm.addStructureViewerListener(this);
       ssm.addSelectionListener(this);
     }
@@ -811,17 +811,20 @@ public class SeqPanel extends JPanel implements MouseListener,
                             .getType()))
             {
               tmpString = features[i].getDescription();
-              int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+              String tmp2up=tmpString.toUpperCase();
+              int startTag = tmp2up.indexOf("<HTML>");
               if (startTag > -1)
               {
                 tmpString = tmpString.substring(startTag + 6);
+                tmp2up = tmp2up.substring(startTag+6);
               }
-              int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+              int endTag = tmp2up.indexOf("</BODY>");
               if (endTag > -1)
               {
                 tmpString = tmpString.substring(0, endTag);
+                tmp2up = tmp2up.substring(0, endTag);
               }
-              endTag = tmpString.toUpperCase().indexOf("</HTML>");
+              endTag = tmp2up.indexOf("</HTML>");
               if (endTag > -1)
               {
                 tmpString = tmpString.substring(0, endTag);