+ if(graph==annotations.getSelectedIndex())\r
+ break;\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = av.alignment.getAlignmentAnnotation()[graph+nograph];\r
+\r
+\r
+ int aboveThreshold = -1;\r
+ if(threshold.getSelectedItem().equals("Above Threshold"))\r
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
+ else if(threshold.getSelectedItem().equals("Below Threshold"))\r
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
+\r
+ if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.graphLines==null)\r