+ /**
+ * change node labels to the annotation referred to by labelClass
+ * TODO: promote to a datamodel modification that can be undone
+ * TODO: make argument one case of a generic transformation function ie { undoStep = apply(Tree, TransformFunction)};
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI() {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy())
+ {
+ String newname=null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq!=null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq.getDBRef(), new String[] {labelClass.toUpperCase()});
+ if (refs!=null)
+ {
+ for (int i=0; i<refs.length;i++)
+ {
+ if (newname == null) {
+ newname = new String(refs[i].getAccessionId());
+ } else {
+ newname = newname +"; "+refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname==null)
+ {
+ SequenceFeature sf[] = sq.getSequenceFeatures();
+ for (int i=0;sf!=null && i<sf.length; i++)
+ {
+ if (sf[i].getType().equals(labelClass))
+ {
+ if (newname==null)
+ {
+ newname = new String(sf[i].getDescription());
+ } else {
+ newname = newname + "; "+sf[i].getDescription();
+ }
+ }
+ }
+ }
+ }
+ if (newname!=null)
+ {
+ String oldname = ((SequenceNode) node).getName();
+ // TODO : save in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
+}
\ No newline at end of file