Set start seq and end seq correctly

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 0307a96..2d2e1ea 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -374,8 +374,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
      width = av.getColumnSelection().findColumnPosition(width);\r
 \r
     av.setStartRes(x);\r
-    av.setStartSeq(y);\r
-\r
     av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);\r
 \r
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;\r
@@ -411,6 +409,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       x = 0;\r
     }\r
 \r
+    av.setStartSeq(y);\r
+\r
     int endSeq = y + vextent;\r
     if (endSeq > av.alignment.getHeight())\r
     {\r
@@ -418,8 +418,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     }\r
 \r
     av.setEndSeq(endSeq);\r
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+    hscroll.setValues(x, hextent, 0, width);\r
+    vscroll.setValues(y, vextent, 0, height);\r
 \r
     if(overviewPanel!=null)\r
           overviewPanel.setBoxPosition();\r