+ for (int i = 0; i < chains.size(); i++)
+ {
+ SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ if (inFile != null)
+ {
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
+ seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D(id);
+ System.out.println(id);
+ //BufferedWriter r = an3d.getReader();
+
+ BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+
+ String str;
+ while ((str = in.readLine()) != null) {
+ System.out.println(str);
+ System.out.println("toto");