Case wrapped jar file, wrapped preference true dealt with

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 67eaef8..c00f29f 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -599,6 +599,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */\r
   public void adjustmentValueChanged(AdjustmentEvent evt)\r
   {\r
+\r
     int oldX = av.getStartRes();\r
     int oldY = av.getStartSeq();\r
 \r
@@ -616,10 +617,26 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
       if (av.getWrapAlignment())\r
       {\r
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
-            seqCanvas.getWidth());\r
-        av.setStartRes(vscroll.getValue() * rowSize);\r
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
+        if(offy>-1)\r
+        {\r
+          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+              seqCanvas.getWidth());\r
+          av.setStartRes(offy * rowSize);\r
+          av.setEndRes( (offy + 1) * rowSize);\r
+        }\r
+        else\r
+        {\r
+          //This is only called if file loaded is a jar file that\r
+          //was wrapped when saved and user has wrap alignment true\r
+          //as preference setting\r
+          SwingUtilities.invokeLater(new Runnable()\r
+              {\r
+                public void run()\r
+                {\r
+                  setScrollValues(av.getStartRes(), av.getStartSeq());\r
+                }\r
+              });\r
+        }\r
       }\r
       else\r
       {\r