}
private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
{
-// System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ // process prot sequence with Jmol to get annotated alignment.
+ // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
}
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");