- AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
- if (bestm==null || aseq.getMaxScore()>bestscore)
+ oldId = "";
+ }
+ aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+ }
+ }
+ }
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+ throws Exception
+ {
+ try
+ {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl != null)
+ {
+ Object jmf = cl.getConstructor(new Class[]
+ { FileParse.class }).newInstance(new Object[]
+ { new FileParse(getDataName(), type) });
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[]
+ {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[]
+ { Alignment.class }).invoke(jmf, al);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ else