- // 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)
- {
- String path =inFile.getPath();
- System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D(path);
- 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");
-
- // }
- //String type = "File";
- //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
- System.out.println("Create rnamfile object");
- //rnaml.parse("temp");
- //this.annotations =rnaml.getAnnot();
-
- }
-
- AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
- if (chainannot != null)
- {
- for (int ai = 0; ai < chainannot.length; ai++)
- {
-
- chainannot[ai].visible = VisibleChainAnnotation;
- annotations.addElement(chainannot[ai]);
- }