+ /**
+ * Predict secondary structure for RNA and/or protein sequences and add as
+ * annotations
+ *
+ * @param rnaSequences
+ * @param proteinSequences
+ */
+ protected void addSecondaryStructure(List<SequenceI> rnaSequences,
+ List<SequenceI> proteinSequences)
+ {
+ /*
+ * Currently using Annotate3D for RNA, but only if the 'use external
+ * prediction' flag is set
+ */
+ if (externalSecondaryStructure && rnaSequences.size() > 0)
+ {
+ try
+ {
+ processPdbFileWithAnnotate3d(rnaSequences);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ }
+
+ /*
+ * Currently using JMol PDB parser for peptide
+ */
+ if (proteinSequences.size() > 0)
+ {
+ try
+ {
+ processWithJmolParser(proteinSequences);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions from Jmol when processing data in pdb file");
+ x.printStackTrace();
+ }
+ }
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ private void processWithJmolParser(List<SequenceI> prot) throws Exception
+ {
+ try
+ {
+
+ Class cl = Class.forName("jalview.ext.jmol.JmolParser");
+ if (cl != null)
+ {
+ final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
+
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
+ .setProcessSecondaryStructure(predictSecondaryStructure);
+ StructureImportSettings
+ .setExternalSecondaryStructure(externalSecondaryStructure);
+ Object jmf = constructor.newInstance(args);
+ AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
+ .invoke(jmf, al);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getAllPDBEntries().clear();
+ }
+ else
+ {
+ sq.getAllPDBEntries().clear();
+ }
+ }
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ StructureImportSettings.setShowSeqFeatures(true);
+ }
+