private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");
Annotate3D an3d = new Annotate3D();
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
}