- List<String> fetchPdbFiles()
- {
- // todo - record which pdbids were successfully imported.
- StringBuilder errormsgs = new StringBuilder();
-
- List<String> files = new ArrayList<String>();
- String pdbid = "";
- try
- {
- String[] filesInViewer = jmb.getPdbFile();
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- Pdb pdbclient = new Pdb();
- for (int pi = 0; pi < jmb.getPdbCount(); pi++)
- {
- String file = jmb.getPdbEntry(pi).getFile();
- if (file == null)
- {
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.getPdbEntry(pi).getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new String[] { pdbid }), hdl);
- }
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'").append(pdbid).append("'");
- } finally
- {
- if (progressBar != null)
- {
- progressBar.setProgressBar(
- MessageManager.getString("label.state_completed"),
- hdl);
- }
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- jmb.getPdbEntry(pi).setFile(file);
- files.add(file);
- }
- else
- {
- errormsgs.append("'").append(pdbid).append("' ");
- }
- }
- else
- {
- if (filesInViewer != null && filesInViewer.length > 0)
- {
- addingStructures = true; // already files loaded.
- for (int c = 0; c < filesInViewer.length; c++)
- {
- if (filesInViewer[c].equals(file))
- {
- file = null;
- break;
- }
- }
- }
- if (file != null)
- {
- files.add(file);
- }
- }
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '")
- .append(pdbid).append("'");
- }
- if (errormsgs.length() > 0)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[] { errormsgs.toString() }),
- MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
- }
- return files;
- }
-
- @Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
- }
-