- Enumeration en = jds.getDatasetSequence().getPDBId().elements();
- while(en.hasMoreElements())
- {
- Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry
- = (jalview.datamodel.PDBEntry)en.nextElement();
-
- pdb.setId(entry.getId());
- pdb.setType(entry.getType());
-
-
- if(entry.getFile()!=null)
- {
- pdb.setFile(entry.getFile());
- if(pdbfiles==null)
- pdbfiles = new Vector();
-
- if(!pdbfiles.contains(entry.getId()))
- {
- pdbfiles.addElement(entry.getId());
- try
- {
- File file = new File(entry.getFile());
- if(file.exists() && jout!=null)
- {
- byte[] data = new byte[ (int) file.length()];
- jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(new
- FileInputStream(file));
- dis.readFully(data);
-
- DataOutputStream dout = new DataOutputStream(jout);
- dout.write(data, 0, data.length);
- jout.closeEntry();
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
-
- if(entry.getProperty()!=null)
- {
- PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
- while(en2.hasMoreElements())
- {
- Property prop = new Property();
- String key = en2.nextElement().toString();
- prop.setName(key);
- prop.setValue( properties.get(key).toString() );
- item.addProperty(prop);
- }
- pdb.addPdbentryItem(item);
- }
-
- jseq.addPdbids(pdb);
- }