- start = location.getBegin().getPosition().intValue();
- end = location.getEnd().getPosition().intValue();
+ if (location.getBegin().getPosition() == null)
+ {
+ Console.warn(
+ "Setting start position of feature with uncertain start to 1: "
+ + uf.getType() + ":" + getDescription(uf));
+ start = sequence.getStart();
+ uncertain_start = location.getBegin().getStatus();
+ }
+ else
+ {
+ start = location.getBegin().getPosition().intValue();
+ }
+ if (location.getEnd().getPosition() == null)
+ {
+ Console.warn(
+ "Setting start position of feature with uncertain start to 1: "
+ + uf.getType() + ":" + getDescription(uf));
+ end = sequence.getEnd();
+ uncertain_end = location.getEnd().getStatus();
+ }
+ else
+ {
+ end = location.getEnd().getPosition().intValue();
+ }