+ LocationType location = uf.getLocation();
+ int start = 0;
+ int end = 0;
+ String uncertain_start = null, uncertain_end = null,
+ uncertain_pos = null;
+ if (location.getPosition() != null)
+ {
+ if (location.getPosition().getPosition() == null
+ || !"unknown".equals(location.getPosition().getStatus()))
+ {
+ Console.warn(
+ "Ignoring single position feature with uncertain location "
+ + uf.getType() + ":" + getDescription(uf));
+ uncertain_pos = location.getPosition().getStatus() == null
+ ? "unknown"
+ : location.getPosition().getStatus();
+ }
+ else
+ {
+ start = location.getPosition().getPosition().intValue();
+ end = start;
+ }
+ }
+ else
+ {
+ 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();
+ }
+ }
+ SequenceFeature sf = new SequenceFeature(uf.getType(),
+ getDescription(uf), start, end, "Uniprot");
+ sf.setStatus(uf.getStatus());
+ if (uncertain_end != null)
+ {
+ sf.setValue("end_status", uncertain_end);
+ }
+ if (uncertain_start != null)
+ {
+ sf.setValue("start_status", uncertain_start);
+ }
+ if (uncertain_pos != null)
+ {
+ sf.setValue("pos_status", uncertain_pos);
+ }