List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager().getRegisteredWorkersOfClass(clientClass);
- JabawsAlignCalcWorker worker;
+ AbstractJabaCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
}
try
{
- worker = (JabawsAlignCalcWorker) (clientClass
+ worker = (AbstractJabaCalcWorker) (clientClass
.getConstructor(new Class[]
{ Jws2Instance.class, AlignFrame.class,
WsParamSetI.class, List.class })
}
else
{
- worker = (JabawsAlignCalcWorker) clnts.get(0);
+ worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
}
}
}
-
- private boolean registerAAConWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; //
- // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
- if (aaui == null)
- {
- // not an instantaneous calculation GUI type service
- return false;
- }
- // create the instaneous calculation GUI bits and update state if existing
- // GUI elements already present
-
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(aaui.getAAconToggle()))
- {
- _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(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient
- .get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- buildCurrentAAConWorkerFor(aaui, 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(
- aaui.getAAconToggle());
-
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip()
- + "</p>") + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip()
- + "</p>") + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(aaui, alignFrame);
- }
- });
- wsmenu.add(modifyParams);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- // TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
- .isNa() : aaui.isPr())
- {
- aaConEnabled.setEnabled(true);
- modifyParams.setEnabled(true);
- }
- else
- {
- aaConEnabled.setEnabled(false);
- modifyParams.setEnabled(false);
- }
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- 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
-
- }
- });
-
- }
- return true;
- }
-
- private static void showAAConAnnotationSettingsFor(
- final AlignAnalysisUIText aaui, 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(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui);
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, 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(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui, 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(
- AlignAnalysisUIText aaui)
- {
- return createDefaultAAConSettings(aaui, null);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- AlignAnalysisUIText aaui, 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,
- aaui.getServiceType());
- }
- 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(AlignAnalysisUIText aaui,
- AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(aaui.getClient());
- }
}
git://source.jalview.org / jalview.git / blobdiff