/** * This method gets rid of an EntryEdit object and it's frame. Each object removed with this * method must have been added previously with addEntryEdit(). * * @param entry_edit The object to get rid of. */ public void entryEditFinished(EntryEdit entry_edit) { if (null == entry_edit) throw new Error("entryEditFinished() was passed a null object"); if (!entry_edit_objects.removeElement(entry_edit)) throw new Error("entryEditFinished() - could not remove a " + "object from an empty vector"); entry_edit.setVisible(false); entry_edit.dispose(); }
/** * Add an EntryEdit object to our list of objects. * * @param entry_edit The object to add. */ public synchronized void addEntryEdit(EntryEdit entry_edit) { entry_edit_objects.addElement(entry_edit); }
/** Read the entries named in args and in the diana.ini file. */ protected void readArgsAndOptions(final String[] args) { if (args.length == 0) { if (System.getProperty("chado") != null && (args.length < 1 || args[0].indexOf(':') == -1)) fm = new LocalAndRemoteFileManager(ArtemisMain.this); // open the entries given in the options file(diana.ini) readDefaultEntries(); return; } if (args[0].equals("-biojava")) { handleBioJava(args); return; } final EntryInformation artemis_entry_information = Options.getArtemisEntryInformation(); EntryEdit last_entry_edit = null; boolean seen_plus = false; for (int i = 0; i < args.length; ++i) { String new_entry_name = args[i]; if (new_entry_name.length() == 0) continue; if (new_entry_name.equals("+")) { seen_plus = true; continue; } if (new_entry_name.startsWith("+") && last_entry_edit != null || seen_plus) { // new feature file final Document entry_document; if (seen_plus) entry_document = DocumentFactory.makeDocument(new_entry_name); else entry_document = DocumentFactory.makeDocument(new_entry_name.substring(1)); final InputStreamProgressListener progress_listener = getInputStreamProgressListener(); entry_document.addInputStreamProgressListener(progress_listener); final uk.ac.sanger.artemis.io.Entry new_embl_entry = EntryFileDialog.getEntryFromFile( this, entry_document, artemis_entry_information, false); if (new_embl_entry == null) // the read failed break; try { final Entry new_entry = new Entry(last_entry_edit.getEntryGroup().getBases(), new_embl_entry); last_entry_edit.getEntryGroup().add(new_entry); } catch (OutOfRangeException e) { new MessageDialog( this, "read failed: one of the features in " + new_entry_name + " has an out of range " + "location: " + e.getMessage()); } } else if (System.getProperty("chado") != null && new_entry_name.indexOf(':') > -1) { // open from database e.g. Pfalciparum:Pf3D7_09:95000..150000 Splash.logger4j.info("OPEN ENTRY " + new_entry_name); getStatusLabel().setText("Connecting ..."); DatabaseEntrySource entry_source = new DatabaseEntrySource(); boolean promptUser = true; if (System.getProperty("read_only") != null) { promptUser = false; entry_source.setReadOnly(true); } if (!entry_source.setLocation(promptUser)) return; last_entry_edit = DatabaseJPanel.show( entry_source, this, getInputStreamProgressListener(), new_entry_name); } else { // new sequence file if (last_entry_edit != null) { last_entry_edit.setVisible(true); last_entry_edit = null; } if (new_entry_name.indexOf("://") == -1) { File file = new File(new_entry_name); if (!file.exists()) { JOptionPane.showMessageDialog( null, "File " + new_entry_name + " not found.\n" + "Check the file name.", "File Not Found", JOptionPane.WARNING_MESSAGE); } } final Document entry_document = DocumentFactory.makeDocument(new_entry_name); entry_document.addInputStreamProgressListener(getInputStreamProgressListener()); final uk.ac.sanger.artemis.io.Entry new_embl_entry = EntryFileDialog.getEntryFromFile( this, entry_document, artemis_entry_information, false); if (new_embl_entry == null) // the read failed break; try { final Entry entry = new Entry(new_embl_entry); last_entry_edit = makeEntryEdit(entry); addEntryEdit(last_entry_edit); getStatusLabel().setText(""); } catch (OutOfRangeException e) { new MessageDialog( this, "read failed: one of the features in " + new_entry_name + " has an out of range " + "location: " + e.getMessage()); break; } catch (NoSequenceException e) { new MessageDialog(this, "read failed: " + new_entry_name + " contains no sequence"); break; } } } if (System.getProperty("offset") != null) last_entry_edit.getGotoEventSource().gotoBase(Integer.parseInt(System.getProperty("offset"))); last_entry_edit.setVisible(true); for (int entry_index = 0; entry_index < entry_edit_objects.size(); ++entry_index) { if (System.getProperty("offset") != null) entry_edit_objects .elementAt(entry_index) .getGotoEventSource() .gotoBase(Integer.parseInt(System.getProperty("offset"))); } }