+
+ viewHeight = av.getEndSeq() - av.getStartSeq();
+ viewWidth = av.getEndRes() - av.getStartRes();
+
+ // wait for gui to get set up
+ while (viewHeight != 17 || viewWidth != 59)
+ {
+ try
+ {
+ Thread.sleep(50);
+ viewHeight = av.getEndSeq() - av.getStartSeq();
+ viewWidth = av.getEndRes() - av.getStartRes();
+ } catch (InterruptedException e)
+ {
+
+ }
+ }
+
+ // calculate before hidden columns so we get absolute values
+ alheight = av.getAlignment().getHeight();
+ alwidth = av.getAlignment().getWidth();
+
+ boxWidth = Math.round((float) (av.getEndRes() - av.getStartRes() + 1)
+ / alwidth * od.getWidth());
+ boxHeight = Math.round((float) (av.getEndSeq() - av.getStartSeq())
+ / alheight * od.getHeight());
+ System.out.println(boxHeight);
+