+ }
+ }
+
+ 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
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void replaceAndUpdateChains(ArrayList<SequenceI> prot,
+ AlignmentI al, String pep, boolean b)
+ {
+ List<List<? extends Object>> replaced = AlignSeq
+ .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+ false);
+ for (PDBChain ch : chains)
+ {
+ int p = 0;
+ for (SequenceI sq : (List<SequenceI>) replaced.get(0))
+ {
+ p++;
+ if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
+ {
+ p = -p;
+ break;
+ }
+ }
+ if (p < 0)
+ {
+ p = -p - 1;
+ // set shadow entry for chains
+ ch.shadow = (SequenceI) replaced.get(1).get(p);
+ ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
+ .getMappingFromS1(false);
+ }
+ }
+ }
+
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
+ throws Exception
+ {
+ // System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run
+ // without the HTTPClient bits and pieces needed for accessing Annotate3D
+ // web service
+ try
+ {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl != null)