- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+ newann=sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup>-1)
+ {
+ if (newann.graphGroup>-1)
+ {
+ if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ {
+ for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ }
+ }