+
+ /*
+ * for sequence_variant, make an additional feature with consequence
+ */
+ if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
+ {
+ String consequence = (String) sf.getValue("consequence_type");
+ if (consequence != null)
+ {
+ SequenceFeature sf2 = new SequenceFeature("consequence",
+ consequence, copy.getBegin(), copy.getEnd(), 0f,
+ null);
+ targetSequence.addSequenceFeature(sf2);
+ }
+ }