vamsasSeq = new Sequence();
vamsasSeq.setId(id + "");
vamsasSeq.setName(jds.getName());
vamsasSeq = new Sequence();
vamsasSeq.setId(id + "");
vamsasSeq.setName(jds.getName());
BufferedReader in = new BufferedReader(new InputStreamReader(jin));
File outFile = File.createTempFile("jalview_pdb", ".txt");
BufferedReader in = new BufferedReader(new InputStreamReader(jin));
File outFile = File.createTempFile("jalview_pdb", ".txt");