-
- private final String AAconToggle = "AACon Calculations",
- AAconToggleTooltip = "When checked, AACon calculations are updated automatically.",
- AAeditSettings = "Change AACon Settings...",
- AAeditSettingsTooltip = "Modify settings for AACon calculations.";
-
- private void registerAAConWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- // register this in the AACon settings set
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(AAconToggle))
- {
- _aaConEnabled = (JCheckBoxMenuItem) item;
- }
- }
- // is there an aaCon worker already present - if so, set it to use the
- // given service handle
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
- if (aaconClient != null && aaconClient.size() > 0)
- {
- AAConClient worker = (AAConClient) aaconClient.get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(alignFrame);
- buildCurrentAAConWorkerFor(alignFrame, service);
- }
- }// );
- }
- }
- }
-
- // is there a service already registered ? there shouldn't be if we are
- // being called correctly
- if (_aaConEnabled == null)
- {
- final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- AAconToggle);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
- .isNucleotide());
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
- if (aaconClient != null && aaconClient.size() > 0)
- {
- aaConEnabled.setSelected(true);
- }
- else
- {
- aaConEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
- });
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
- + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConClient.class);
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- JMenuItem modifyParams = new JMenuItem(AAeditSettings);
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(alignFrame);
- }
- });
- wsmenu.add(modifyParams);
-
- }
- }
-
- private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- // could actually do a class search for this too
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConCalcId);
- if (fave == null)
- {
- fave = createDefaultAAConSettings();
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame,
- Jws2Instance service)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConCalcId);
- if (fave == null)
- {
- fave = createDefaultAAConSettings(service);
- }
- else
- {
- if (service != null
- && !fave.getService().hosturl.equals(service.hosturl))
- {
- Cache.log.debug("Changing AACon service to " + service.hosturl
- + " from " + fave.getService().hosturl);
- fave.setService(service);
- }
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConSettings createDefaultAAConSettings()
- {
- return createDefaultAAConSettings(null);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- Jws2Instance service)
- {
- if (service != null)
- {
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
- {
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
- + service.serviceType + ")");
- service = null;
- }
- else
- {
- // check service is actually in the list of currently avaialable
- // services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
- {
- // it isn't ..
- service = null;
- }
- }
- }
- if (service == null)
- {
- // get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- compbio.ws.client.Services.AAConWS.toString());
- }
- if (service == null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA
- // preferences menu.
- throw new Error("No AACon service found.");
- }
- return new AAConSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(AAConClient.class);
- }