cutStartPos, cutEndPos);
/*
+ * add any contact features that span the cut region
+ * (not returned by findFeatures)
+ */
+ for (SequenceFeature contact : featureStore.getContactFeatures())
+ {
+ if (contact.getBegin() < cutStartPos
+ && contact.getEnd() > cutEndPos)
+ {
+ toAmend.add(contact);
+ }
+ }
+
+ /*
* adjust start-end of overlapping features;
* delete features enclosed by the cut;
* delete partially overlapping contact features